Aaron Lun
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/csaw |
| Branch: RELEASE_3_6 |
| Last Commit: c9f2f1a |
| Last Changed Date: 2017-10-30 12:40:43 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:25:13 -0400 (Thu, 12 Apr 2018).
| Package 314/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| csaw 1.12.0 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: csaw |
| Version: 1.12.0 |
| Command: rm -rf csaw.buildbin-libdir csaw.Rcheck && mkdir csaw.buildbin-libdir csaw.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=csaw.buildbin-libdir csaw_1.12.0.tar.gz >csaw.Rcheck\00install.out 2>&1 && cp csaw.Rcheck\00install.out csaw-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=csaw.buildbin-libdir --install="check:csaw-install.out" --force-multiarch --no-vignettes --timings csaw_1.12.0.tar.gz |
| StartedAt: 2018-04-11 23:17:32 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:26:25 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 532.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: csaw.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf csaw.buildbin-libdir csaw.Rcheck && mkdir csaw.buildbin-libdir csaw.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=csaw.buildbin-libdir csaw_1.12.0.tar.gz >csaw.Rcheck\00install.out 2>&1 && cp csaw.Rcheck\00install.out csaw-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=csaw.buildbin-libdir --install="check:csaw-install.out" --force-multiarch --no-vignettes --timings csaw_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/csaw.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'csaw/DESCRIPTION' ... OK
* this is package 'csaw' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'csaw' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/csaw.buildbin-libdir/csaw/libs/i386/csaw.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
detailRanges 10.61 0.38 10.99
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
detailRanges 13.97 0.25 14.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-basic.R'
Comparing 'test-basic.Rout' to 'test-basic.Rout.save' ...255,258d254
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
261,264d256
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
267,270d258
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
296,299d283
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
308,311d291
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
Warning message:
running command '"diff" -bw "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpUJl7e5\Rdiffa261c6f84c62" "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpUJl7e5\Rdiffb261c5d887196"' had status 1
OK
** running tests for arch 'x64' ...
Running 'test-basic.R'
Comparing 'test-basic.Rout' to 'test-basic.Rout.save' ...255,258d254
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
261,264d256
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
267,270d258
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
296,299d283
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
308,311d291
< Warning message:
< 'se.out=NULL' is deprecated.
< Use 'se.out=TRUE' instead.
< See help("Deprecated")
Warning message:
running command '"diff" -bw "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpcRu9AT\Rdiffac1454621bc5" "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpcRu9AT\Rdiffbc1470532e6d"' had status 1
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/csaw.Rcheck/00check.log'
for details.
csaw.Rcheck/00install.out
install for i386
* installing *source* package 'csaw' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c annotator.cpp -o annotator.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c bam_utils.cpp -o bam_utils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c best_in_cluster.cpp -o best_in_cluster.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c check_bimodality.cpp -o check_bimodality.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c correlate_reads.cpp -o correlate_reads.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c find_maxima.cpp -o find_maxima.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_cluster_stats.cpp -o get_cluster_stats.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_profile.cpp -o get_profile.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_rle_counts.cpp -o get_rle_counts.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c merge_windows.cpp -o merge_windows.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c pair_reads.cpp -o pair_reads.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c single_reads.cpp -o single_reads.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o csaw.dll tmp.def annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o utils.o -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/csaw.buildbin-libdir/csaw/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'csaw'
finding HTML links ... done
SEmethods html
finding level-2 HTML links ... done
checkBimodality html
clusterFDR html
clusterWindows html
combineTests html
consolidateClusters html
consolidateSizes html
correlateReads html
csawUsersGuide html
detailRanges html
empiricalFDR html
extractReads html
filterWindows html
findMaxima html
getBestTest html
getPESizes html
getWidths html
maximizeCcf html
mergeWindows html
mixedClusters html
normOffsets html
overlapStats html
profileSites html
readParam html
regionCounts html
scaledAverage html
strandedCounts html
upweightSummit html
windowCounts html
wwhm html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'csaw' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c annotator.cpp -o annotator.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c bam_utils.cpp -o bam_utils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c best_in_cluster.cpp -o best_in_cluster.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c check_bimodality.cpp -o check_bimodality.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c correlate_reads.cpp -o correlate_reads.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c find_maxima.cpp -o find_maxima.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_cluster_stats.cpp -o get_cluster_stats.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_profile.cpp -o get_profile.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c get_rle_counts.cpp -o get_rle_counts.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c merge_windows.cpp -o merge_windows.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c pair_reads.cpp -o pair_reads.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c single_reads.cpp -o single_reads.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o csaw.dll tmp.def annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o utils.o -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/csaw.buildbin-libdir/csaw/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'csaw' as csaw_1.12.0.zip
* DONE (csaw)
In R CMD INSTALL
In R CMD INSTALL
|
csaw.Rcheck/tests_i386/test-basic.Rout.save
R Under development (unstable) (2016-10-17 r71531) -- "Unsuffered Consequences"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This is a testing stub that just provides a basic run-through of all the methods.
> # The real tests are located in inst/tests along with a Bash script for execution
> # and comparison. The separation into two folders is necessary to keep R CMD check
> # running with reasonable speed.
>
> suppressWarnings(suppressPackageStartupMessages(require(csaw)))
> both.files <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
> pe.file <- system.file("exdata", "pet.bam", package="csaw")
>
> # Checking data quality prior to counting.
> head(correlateReads(both.files))
[1] -0.0137654663 0.0005571408 0.0175021237 -0.0308470292 -0.0087488234
[6] -0.0120687468
> head(correlateReads(both.files, cross=FALSE))
[1] 1.0000000000 -0.0008601215 0.0170688852 -0.0475443596 0.0028128511
[6] -0.0030687197
>
> getPESizes(pe.file)
$sizes
[1] 70 90 20 150 10 30 10 2
$diagnostics
total.reads mapped.reads single mate.unmapped unoriented
23 23 3 0 1
inter.chr
1
>
> # Trying to count some single-end data.
> data <- windowCounts(both.files, ext=100)
> head(assay(data))
[,1] [,2]
[1,] 43 71
[2,] 57 89
[3,] 56 120
[4,] 53 141
[5,] 40 152
[6,] 59 135
> rowRanges(data)
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, width=500, spacing=200)
> head(assay(data))
[,1] [,2]
[1,] 204 455
[2,] 195 510
[3,] 186 483
[4,] 200 501
[5,] 187 468
[6,] 127 311
> rowRanges(data)
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 500] *
[2] chrA [201, 700] *
[3] chrA [401, 900] *
[4] chrA [601, 1100] *
[5] chrA [801, 1298] *
... ... ... ...
[15] chrC [ 401, 900] *
[16] chrC [ 601, 1100] *
[17] chrC [ 801, 1300] *
[18] chrC [1001, 1345] *
[19] chrC [1201, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100))
> data$totals
[1] 914 2152
> data <- windowCounts(both.files, ext=100, param=readParam(dedup=TRUE))
> data$totals
[1] 1056 2582
> data <- windowCounts(both.files, ext=100, param=readParam(discard=GRanges("chrA", IRanges(50, 500))))
> data$totals
[1] 1186 2916
> data <- windowCounts(both.files, ext=100, param=readParam(restrict="chrA"))
> data$totals
[1] 451 1093
>
> # Trying to count some paired-end data.
> out <- windowCounts(pe.file, param=readParam(pe="both"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 2
[4,] 1
[5,] 4
[6,] 3
> out$totals
[1] 8
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="both", max.frag=100), width=100, filter=1L)
> assay(out)
[,1]
[1,] 2
[2,] 3
[3,] 1
[4,] 4
[5,] 3
> out$totals
[1] 7
> rowRanges(out)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrB [ 1, 100] *
[5] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="first"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 4
[4,] 2
[5,] 6
[6,] 6
> out$totals
[1] 10
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
>
> # Trying to convert it to a DGEList.
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 1
> asDGEList(data, lib.size=c(10, 10))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 10 1
Sample2 1 10 1
> asDGEList(data, norm=c(1,2))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 2
>
> temp <- data
> temp$totals <- NULL
> asDGEList(temp) # Should spit out a warning.
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 1293 1
Sample2 1 3142 1
Warning message:
In .local(object, ...) :
library sizes not found in 'totals', setting to NULL
>
> # Running some basic normalization.
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100, dedup=TRUE))
>
> normOffsets(assay(data), lib.size=data$totals)
[1] 1.001197 0.998804
> normOffsets(assay(data), lib.size=data$totals, logratioTrim=.2)
[1] 1.003816 0.996199
> normOffsets(assay(data), lib.size=data$totals, method="RLE")
[1] 1.0037890 0.9962253
> normOffsets(data)
[1] 1.001197 0.998804
> normOffsets(data, logratioTrim=0.1)
[1] 1.0026764 0.9973307
> normOffsets(data, method="upperquartile")
[1] 0.9834651 1.0168129
>
> head(normOffsets(assay(data), lib.size=data$totals, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
> head(normOffsets(assay(data), lib.size=data$totals, type="loess", span=0.7))
[,1] [,2]
[1,] -0.4297765 0.4297765
[2,] -0.4391936 0.4391936
[3,] -0.3867962 0.3867962
[4,] -0.4215479 0.4215479
[5,] -0.3858107 0.3858107
[6,] -0.3915074 0.3915074
> head(normOffsets(data, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
> head(normOffsets(data, type="loess", span=0.5))
[,1] [,2]
[1,] -0.4120470 0.4120470
[2,] -0.4350054 0.4350054
[3,] -0.3740611 0.3740611
[4,] -0.4122536 0.4122536
[5,] -0.3722926 0.3722926
[6,] -0.3835921 0.3835921
>
> # Assuming someone went around and pulled out some p-values for everybody.
> set.seed(128145-19238)
> nr <- nrow(data)
> tabled <- data.frame(logFC=rnorm(nr), logCPM=rnorm(nr), PValue=rbeta(nr, 1, 2))
> weighting <- rgamma(nr, 2, 1)
>
> mergeWindows(rowRanges(data), -1)
$id
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
[51] 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
$region
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100)
$id
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2
[39] 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
$region
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [1, 1298] *
[2] chrB [1, 870] *
[3] chrC [1, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100, max.width=500)
$id
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 5 5 5
[39] 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8
$region
GRanges object with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 450] *
[2] chrA [451, 850] *
[3] chrA [851, 1298] *
[4] chrB [ 1, 450] *
[5] chrB [451, 870] *
[6] chrC [ 1, 450] *
[7] chrC [451, 900] *
[8] chrC [901, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> merged <- mergeWindows(rowRanges(data), 100, sign=tabled$logFC > 0)
> merged
$id
[1] 1 2 2 3 4 4 4 5 5 6 7 8 9 9 9 9 10 10 11 12 13 14 15 15 15
[26] 15 16 17 18 18 18 18 18 19 19 20 21 22 23 24 24 25 25 26 27 28 29 29 30 30
[51] 31 31 31 31 32 33 34 34 34 34 35 36 37 37 38 39 40 41 41 42 43
$region
GRanges object with 43 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 150] *
[3] chrA [151, 200] *
[4] chrA [201, 350] *
[5] chrA [351, 450] *
... ... ... ...
[39] chrC [1051, 1100] *
[40] chrC [1101, 1150] *
[41] chrC [1151, 1250] *
[42] chrC [1251, 1300] *
[43] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
>
> head(combineTests(merged$id, tabled))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5047602 up
4 3 0 1 0.08956765 0.4125151 down
5 2 1 0 0.28172663 0.5047602 up
6 1 0 1 0.01949563 0.4125151 down
> head(combineTests(merged$id, tabled, weight=weighting))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5228651 up
4 3 0 1 0.04669873 0.4255938 down
5 2 1 0 0.24536526 0.4795776 up
6 1 0 1 0.01949563 0.3373185 down
>
> head(getBestTest(merged$id, tabled))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 3 -0.24872062 -0.73322697 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5047602
4 5 -0.01753979 1.78172679 0.08956765 0.4442470
5 9 0.21512818 1.42847478 0.28172663 0.5047602
6 10 -1.10068046 -0.09313516 0.01949563 0.4442470
> head(getBestTest(merged$id, tabled, weight=weighting))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 2 -0.41696325 1.60566251 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.04669873 0.4255938
5 9 0.21512818 1.42847478 0.24536526 0.4795776
6 10 -1.10068046 -0.09313516 0.01949563 0.3373185
> head(getBestTest(merged$id, tabled, by.pval=FALSE))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5622769
2 2 -0.41696325 1.60566251 0.79272727 0.8116017
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.02985588 0.2567606
5 9 0.21512818 1.42847478 0.14086332 0.4038082
6 10 -1.10068046 -0.09313516 0.01949563 0.2567606
>
> # Pulling out some diagnostics.
> suppressPackageStartupMessages(require(org.Mm.eg.db))
> suppressPackageStartupMessages(require(TxDb.Mmusculus.UCSC.mm10.knownGene))
>
> current <- readRDS(system.file("exdata", "exrange.rds", package="csaw"))
> output <- detailRanges(current, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db)
> head(output$overlap)
[1] "Nrxn3|8|+" "" ""
[4] "1700007G11Rik|I|+" "Mannr|2|+" ""
> head(output$right)
[1] "Nrxn3|9|+[3846]" "Rprm|1|-[2293]" "" ""
[5] "" ""
> head(output$left)
[1] "" ""
[3] "" "1700007G11Rik|5|+[2890]"
[5] "" ""
>
> # Pulling out some reads.
> extractReads(both.files[1], GRanges("chrA", IRanges(100, 500)))
GRanges object with 143 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 94, 103] +
[2] chrA [106, 115] +
[3] chrA [120, 129] +
[4] chrA [120, 129] +
[5] chrA [129, 138] +
... ... ... ...
[139] chrA [467, 476] -
[140] chrA [482, 491] -
[141] chrA [490, 499] -
[142] chrA [491, 500] -
[143] chrA [499, 508] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)))
GRanges object with 27 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [43, 52] +
[2] chrA [51, 60] +
[3] chrA [57, 66] +
[4] chrA [62, 71] +
[5] chrA [63, 72] +
... ... ... ...
[23] chrA [79, 88] -
[24] chrA [83, 92] -
[25] chrA [88, 97] -
[26] chrA [89, 98] -
[27] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)), param=readParam(dedup=TRUE))
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [51, 60] +
[2] chrA [57, 66] +
[3] chrA [62, 71] +
[4] chrA [63, 72] +
[5] chrA [76, 85] +
... ... ... ...
[15] chrA [79, 88] -
[16] chrA [79, 88] -
[17] chrA [88, 97] -
[18] chrA [89, 98] -
[19] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="both"))
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [50, 79] *
[2] chrB [90, 99] *
[3] chrB [99, 100] *
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="second"))
GRanges object with 4 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [75, 84] +
[2] chrB [90, 99] +
[3] chrB [70, 79] -
[4] chrB [99, 100] -
-------
seqinfo: 1 sequence from an unspecified genome
>
>
> proc.time()
user system elapsed
14.248 0.228 14.563
|
csaw.Rcheck/tests_x64/test-basic.Rout.save
R Under development (unstable) (2016-10-17 r71531) -- "Unsuffered Consequences"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This is a testing stub that just provides a basic run-through of all the methods.
> # The real tests are located in inst/tests along with a Bash script for execution
> # and comparison. The separation into two folders is necessary to keep R CMD check
> # running with reasonable speed.
>
> suppressWarnings(suppressPackageStartupMessages(require(csaw)))
> both.files <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
> pe.file <- system.file("exdata", "pet.bam", package="csaw")
>
> # Checking data quality prior to counting.
> head(correlateReads(both.files))
[1] -0.0137654663 0.0005571408 0.0175021237 -0.0308470292 -0.0087488234
[6] -0.0120687468
> head(correlateReads(both.files, cross=FALSE))
[1] 1.0000000000 -0.0008601215 0.0170688852 -0.0475443596 0.0028128511
[6] -0.0030687197
>
> getPESizes(pe.file)
$sizes
[1] 70 90 20 150 10 30 10 2
$diagnostics
total.reads mapped.reads single mate.unmapped unoriented
23 23 3 0 1
inter.chr
1
>
> # Trying to count some single-end data.
> data <- windowCounts(both.files, ext=100)
> head(assay(data))
[,1] [,2]
[1,] 43 71
[2,] 57 89
[3,] 56 120
[4,] 53 141
[5,] 40 152
[6,] 59 135
> rowRanges(data)
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, width=500, spacing=200)
> head(assay(data))
[,1] [,2]
[1,] 204 455
[2,] 195 510
[3,] 186 483
[4,] 200 501
[5,] 187 468
[6,] 127 311
> rowRanges(data)
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 500] *
[2] chrA [201, 700] *
[3] chrA [401, 900] *
[4] chrA [601, 1100] *
[5] chrA [801, 1298] *
... ... ... ...
[15] chrC [ 401, 900] *
[16] chrC [ 601, 1100] *
[17] chrC [ 801, 1300] *
[18] chrC [1001, 1345] *
[19] chrC [1201, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100))
> data$totals
[1] 914 2152
> data <- windowCounts(both.files, ext=100, param=readParam(dedup=TRUE))
> data$totals
[1] 1056 2582
> data <- windowCounts(both.files, ext=100, param=readParam(discard=GRanges("chrA", IRanges(50, 500))))
> data$totals
[1] 1186 2916
> data <- windowCounts(both.files, ext=100, param=readParam(restrict="chrA"))
> data$totals
[1] 451 1093
>
> # Trying to count some paired-end data.
> out <- windowCounts(pe.file, param=readParam(pe="both"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 2
[4,] 1
[5,] 4
[6,] 3
> out$totals
[1] 8
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="both", max.frag=100), width=100, filter=1L)
> assay(out)
[,1]
[1,] 2
[2,] 3
[3,] 1
[4,] 4
[5,] 3
> out$totals
[1] 7
> rowRanges(out)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrB [ 1, 100] *
[5] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="first"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 4
[4,] 2
[5,] 6
[6,] 6
> out$totals
[1] 10
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
>
> # Trying to convert it to a DGEList.
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 1
> asDGEList(data, lib.size=c(10, 10))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 10 1
Sample2 1 10 1
> asDGEList(data, norm=c(1,2))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 2
>
> temp <- data
> temp$totals <- NULL
> asDGEList(temp) # Should spit out a warning.
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 1293 1
Sample2 1 3142 1
Warning message:
In .local(object, ...) :
library sizes not found in 'totals', setting to NULL
>
> # Running some basic normalization.
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100, dedup=TRUE))
>
> normOffsets(assay(data), lib.size=data$totals)
[1] 1.001197 0.998804
> normOffsets(assay(data), lib.size=data$totals, logratioTrim=.2)
[1] 1.003816 0.996199
> normOffsets(assay(data), lib.size=data$totals, method="RLE")
[1] 1.0037890 0.9962253
> normOffsets(data)
[1] 1.001197 0.998804
> normOffsets(data, logratioTrim=0.1)
[1] 1.0026764 0.9973307
> normOffsets(data, method="upperquartile")
[1] 0.9834651 1.0168129
>
> head(normOffsets(assay(data), lib.size=data$totals, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
> head(normOffsets(assay(data), lib.size=data$totals, type="loess", span=0.7))
[,1] [,2]
[1,] -0.4297765 0.4297765
[2,] -0.4391936 0.4391936
[3,] -0.3867962 0.3867962
[4,] -0.4215479 0.4215479
[5,] -0.3858107 0.3858107
[6,] -0.3915074 0.3915074
> head(normOffsets(data, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
> head(normOffsets(data, type="loess", span=0.5))
[,1] [,2]
[1,] -0.4120470 0.4120470
[2,] -0.4350054 0.4350054
[3,] -0.3740611 0.3740611
[4,] -0.4122536 0.4122536
[5,] -0.3722926 0.3722926
[6,] -0.3835921 0.3835921
>
> # Assuming someone went around and pulled out some p-values for everybody.
> set.seed(128145-19238)
> nr <- nrow(data)
> tabled <- data.frame(logFC=rnorm(nr), logCPM=rnorm(nr), PValue=rbeta(nr, 1, 2))
> weighting <- rgamma(nr, 2, 1)
>
> mergeWindows(rowRanges(data), -1)
$id
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
[51] 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
$region
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100)
$id
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2
[39] 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
$region
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [1, 1298] *
[2] chrB [1, 870] *
[3] chrC [1, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100, max.width=500)
$id
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 5 5 5
[39] 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8
$region
GRanges object with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 450] *
[2] chrA [451, 850] *
[3] chrA [851, 1298] *
[4] chrB [ 1, 450] *
[5] chrB [451, 870] *
[6] chrC [ 1, 450] *
[7] chrC [451, 900] *
[8] chrC [901, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> merged <- mergeWindows(rowRanges(data), 100, sign=tabled$logFC > 0)
> merged
$id
[1] 1 2 2 3 4 4 4 5 5 6 7 8 9 9 9 9 10 10 11 12 13 14 15 15 15
[26] 15 16 17 18 18 18 18 18 19 19 20 21 22 23 24 24 25 25 26 27 28 29 29 30 30
[51] 31 31 31 31 32 33 34 34 34 34 35 36 37 37 38 39 40 41 41 42 43
$region
GRanges object with 43 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 150] *
[3] chrA [151, 200] *
[4] chrA [201, 350] *
[5] chrA [351, 450] *
... ... ... ...
[39] chrC [1051, 1100] *
[40] chrC [1101, 1150] *
[41] chrC [1151, 1250] *
[42] chrC [1251, 1300] *
[43] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
>
> head(combineTests(merged$id, tabled))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5047602 up
4 3 0 1 0.08956765 0.4125151 down
5 2 1 0 0.28172663 0.5047602 up
6 1 0 1 0.01949563 0.4125151 down
> head(combineTests(merged$id, tabled, weight=weighting))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5228651 up
4 3 0 1 0.04669873 0.4255938 down
5 2 1 0 0.24536526 0.4795776 up
6 1 0 1 0.01949563 0.3373185 down
>
> head(getBestTest(merged$id, tabled))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 3 -0.24872062 -0.73322697 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5047602
4 5 -0.01753979 1.78172679 0.08956765 0.4442470
5 9 0.21512818 1.42847478 0.28172663 0.5047602
6 10 -1.10068046 -0.09313516 0.01949563 0.4442470
> head(getBestTest(merged$id, tabled, weight=weighting))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 2 -0.41696325 1.60566251 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.04669873 0.4255938
5 9 0.21512818 1.42847478 0.24536526 0.4795776
6 10 -1.10068046 -0.09313516 0.01949563 0.3373185
> head(getBestTest(merged$id, tabled, by.pval=FALSE))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5622769
2 2 -0.41696325 1.60566251 0.79272727 0.8116017
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.02985588 0.2567606
5 9 0.21512818 1.42847478 0.14086332 0.4038082
6 10 -1.10068046 -0.09313516 0.01949563 0.2567606
>
> # Pulling out some diagnostics.
> suppressPackageStartupMessages(require(org.Mm.eg.db))
> suppressPackageStartupMessages(require(TxDb.Mmusculus.UCSC.mm10.knownGene))
>
> current <- readRDS(system.file("exdata", "exrange.rds", package="csaw"))
> output <- detailRanges(current, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db)
> head(output$overlap)
[1] "Nrxn3|8|+" "" ""
[4] "1700007G11Rik|I|+" "Mannr|2|+" ""
> head(output$right)
[1] "Nrxn3|9|+[3846]" "Rprm|1|-[2293]" "" ""
[5] "" ""
> head(output$left)
[1] "" ""
[3] "" "1700007G11Rik|5|+[2890]"
[5] "" ""
>
> # Pulling out some reads.
> extractReads(both.files[1], GRanges("chrA", IRanges(100, 500)))
GRanges object with 143 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 94, 103] +
[2] chrA [106, 115] +
[3] chrA [120, 129] +
[4] chrA [120, 129] +
[5] chrA [129, 138] +
... ... ... ...
[139] chrA [467, 476] -
[140] chrA [482, 491] -
[141] chrA [490, 499] -
[142] chrA [491, 500] -
[143] chrA [499, 508] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)))
GRanges object with 27 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [43, 52] +
[2] chrA [51, 60] +
[3] chrA [57, 66] +
[4] chrA [62, 71] +
[5] chrA [63, 72] +
... ... ... ...
[23] chrA [79, 88] -
[24] chrA [83, 92] -
[25] chrA [88, 97] -
[26] chrA [89, 98] -
[27] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)), param=readParam(dedup=TRUE))
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [51, 60] +
[2] chrA [57, 66] +
[3] chrA [62, 71] +
[4] chrA [63, 72] +
[5] chrA [76, 85] +
... ... ... ...
[15] chrA [79, 88] -
[16] chrA [79, 88] -
[17] chrA [88, 97] -
[18] chrA [89, 98] -
[19] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="both"))
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [50, 79] *
[2] chrB [90, 99] *
[3] chrB [99, 100] *
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="second"))
GRanges object with 4 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [75, 84] +
[2] chrB [90, 99] +
[3] chrB [70, 79] -
[4] chrB [99, 100] -
-------
seqinfo: 1 sequence from an unspecified genome
>
>
> proc.time()
user system elapsed
14.248 0.228 14.563
|
|
csaw.Rcheck/tests_i386/test-basic.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This is a testing stub that just provides a basic run-through of all the methods.
> # The real tests are located in inst/tests along with a Bash script for execution
> # and comparison. The separation into two folders is necessary to keep R CMD check
> # running with reasonable speed.
>
> suppressWarnings(suppressPackageStartupMessages(require(csaw)))
> both.files <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
> pe.file <- system.file("exdata", "pet.bam", package="csaw")
>
> # Checking data quality prior to counting.
> head(correlateReads(both.files))
[1] -0.0137654663 0.0005571408 0.0175021237 -0.0308470292 -0.0087488234
[6] -0.0120687468
> head(correlateReads(both.files, cross=FALSE))
[1] 1.0000000000 -0.0008601215 0.0170688852 -0.0475443596 0.0028128511
[6] -0.0030687197
>
> getPESizes(pe.file)
$sizes
[1] 70 90 20 150 10 30 10 2
$diagnostics
total.reads mapped.reads single mate.unmapped unoriented
23 23 3 0 1
inter.chr
1
>
> # Trying to count some single-end data.
> data <- windowCounts(both.files, ext=100)
> head(assay(data))
[,1] [,2]
[1,] 43 71
[2,] 57 89
[3,] 56 120
[4,] 53 141
[5,] 40 152
[6,] 59 135
> rowRanges(data)
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, width=500, spacing=200)
> head(assay(data))
[,1] [,2]
[1,] 204 455
[2,] 195 510
[3,] 186 483
[4,] 200 501
[5,] 187 468
[6,] 127 311
> rowRanges(data)
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 500] *
[2] chrA [201, 700] *
[3] chrA [401, 900] *
[4] chrA [601, 1100] *
[5] chrA [801, 1298] *
... ... ... ...
[15] chrC [ 401, 900] *
[16] chrC [ 601, 1100] *
[17] chrC [ 801, 1300] *
[18] chrC [1001, 1345] *
[19] chrC [1201, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100))
> data$totals
[1] 914 2152
> data <- windowCounts(both.files, ext=100, param=readParam(dedup=TRUE))
> data$totals
[1] 1056 2582
> data <- windowCounts(both.files, ext=100, param=readParam(discard=GRanges("chrA", IRanges(50, 500))))
> data$totals
[1] 1186 2916
> data <- windowCounts(both.files, ext=100, param=readParam(restrict="chrA"))
> data$totals
[1] 451 1093
>
> # Trying to count some paired-end data.
> out <- windowCounts(pe.file, param=readParam(pe="both"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 2
[4,] 1
[5,] 4
[6,] 3
> out$totals
[1] 8
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="both", max.frag=100), width=100, filter=1L)
> assay(out)
[,1]
[1,] 2
[2,] 3
[3,] 1
[4,] 4
[5,] 3
> out$totals
[1] 7
> rowRanges(out)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrB [ 1, 100] *
[5] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="first"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 4
[4,] 2
[5,] 6
[6,] 6
> out$totals
[1] 10
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
>
> # Trying to convert it to a DGEList.
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 1
> asDGEList(data, lib.size=c(10, 10))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 10 1
Sample2 1 10 1
> asDGEList(data, norm=c(1,2))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 2
>
> temp <- data
> temp$totals <- NULL
> asDGEList(temp) # Should spit out a warning.
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 1293 1
Sample2 1 3142 1
Warning message:
In .local(object, ...) :
library sizes not found in 'totals', setting to NULL
>
> # Running some basic normalization.
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100, dedup=TRUE))
>
> normOffsets(assay(data), lib.size=data$totals)
[1] 1.001197 0.998804
> normOffsets(assay(data), lib.size=data$totals, logratioTrim=.2)
[1] 1.003816 0.996199
> normOffsets(assay(data), lib.size=data$totals, method="RLE")
[1] 1.0037890 0.9962253
> normOffsets(data)
[1] 1.001197 0.998804
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
> normOffsets(data, logratioTrim=0.1)
[1] 1.0026764 0.9973307
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
> normOffsets(data, method="upperquartile")
[1] 0.9834651 1.0168129
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
>
> head(normOffsets(assay(data), lib.size=data$totals, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
> head(normOffsets(assay(data), lib.size=data$totals, type="loess", span=0.7))
[,1] [,2]
[1,] -0.4297765 0.4297765
[2,] -0.4391936 0.4391936
[3,] -0.3867962 0.3867962
[4,] -0.4215479 0.4215479
[5,] -0.3858107 0.3858107
[6,] -0.3915074 0.3915074
> head(normOffsets(data, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
> head(normOffsets(data, type="loess", span=0.5))
[,1] [,2]
[1,] -0.4120470 0.4120470
[2,] -0.4350054 0.4350054
[3,] -0.3740611 0.3740611
[4,] -0.4122536 0.4122536
[5,] -0.3722926 0.3722926
[6,] -0.3835921 0.3835921
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
>
> # Assuming someone went around and pulled out some p-values for everybody.
> set.seed(128145-19238)
> nr <- nrow(data)
> tabled <- data.frame(logFC=rnorm(nr), logCPM=rnorm(nr), PValue=rbeta(nr, 1, 2))
> weighting <- rgamma(nr, 2, 1)
>
> mergeWindows(rowRanges(data), -1)
$id
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
[51] 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
$region
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100)
$id
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2
[39] 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
$region
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [1, 1298] *
[2] chrB [1, 870] *
[3] chrC [1, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100, max.width=500)
$id
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 5 5 5
[39] 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8
$region
GRanges object with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 450] *
[2] chrA [451, 850] *
[3] chrA [851, 1298] *
[4] chrB [ 1, 450] *
[5] chrB [451, 870] *
[6] chrC [ 1, 450] *
[7] chrC [451, 900] *
[8] chrC [901, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> merged <- mergeWindows(rowRanges(data), 100, sign=tabled$logFC > 0)
> merged
$id
[1] 1 2 2 3 4 4 4 5 5 6 7 8 9 9 9 9 10 10 11 12 13 14 15 15 15
[26] 15 16 17 18 18 18 18 18 19 19 20 21 22 23 24 24 25 25 26 27 28 29 29 30 30
[51] 31 31 31 31 32 33 34 34 34 34 35 36 37 37 38 39 40 41 41 42 43
$region
GRanges object with 43 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 150] *
[3] chrA [151, 200] *
[4] chrA [201, 350] *
[5] chrA [351, 450] *
... ... ... ...
[39] chrC [1051, 1100] *
[40] chrC [1101, 1150] *
[41] chrC [1151, 1250] *
[42] chrC [1251, 1300] *
[43] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
>
> head(combineTests(merged$id, tabled))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5047602 up
4 3 0 1 0.08956765 0.4125151 down
5 2 1 0 0.28172663 0.5047602 up
6 1 0 1 0.01949563 0.4125151 down
> head(combineTests(merged$id, tabled, weight=weighting))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5228651 up
4 3 0 1 0.04669873 0.4255938 down
5 2 1 0 0.24536526 0.4795776 up
6 1 0 1 0.01949563 0.3373185 down
>
> head(getBestTest(merged$id, tabled))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 3 -0.24872062 -0.73322697 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5047602
4 5 -0.01753979 1.78172679 0.08956765 0.4442470
5 9 0.21512818 1.42847478 0.28172663 0.5047602
6 10 -1.10068046 -0.09313516 0.01949563 0.4442470
> head(getBestTest(merged$id, tabled, weight=weighting))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 2 -0.41696325 1.60566251 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.04669873 0.4255938
5 9 0.21512818 1.42847478 0.24536526 0.4795776
6 10 -1.10068046 -0.09313516 0.01949563 0.3373185
> head(getBestTest(merged$id, tabled, by.pval=FALSE))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5622769
2 2 -0.41696325 1.60566251 0.79272727 0.8116017
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.02985588 0.2567606
5 9 0.21512818 1.42847478 0.14086332 0.4038082
6 10 -1.10068046 -0.09313516 0.01949563 0.2567606
>
> # Pulling out some diagnostics.
> suppressPackageStartupMessages(require(org.Mm.eg.db))
> suppressPackageStartupMessages(require(TxDb.Mmusculus.UCSC.mm10.knownGene))
>
> current <- readRDS(system.file("exdata", "exrange.rds", package="csaw"))
> output <- detailRanges(current, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db)
> head(output$overlap)
[1] "Nrxn3|8|+" "" ""
[4] "1700007G11Rik|I|+" "Mannr|2|+" ""
> head(output$right)
[1] "Nrxn3|9|+[3846]" "Rprm|1|-[2293]" "" ""
[5] "" ""
> head(output$left)
[1] "" ""
[3] "" "1700007G11Rik|5|+[2890]"
[5] "" ""
>
> # Pulling out some reads.
> extractReads(both.files[1], GRanges("chrA", IRanges(100, 500)))
GRanges object with 143 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 94, 103] +
[2] chrA [106, 115] +
[3] chrA [120, 129] +
[4] chrA [120, 129] +
[5] chrA [129, 138] +
... ... ... ...
[139] chrA [467, 476] -
[140] chrA [482, 491] -
[141] chrA [490, 499] -
[142] chrA [491, 500] -
[143] chrA [499, 508] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)))
GRanges object with 27 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [43, 52] +
[2] chrA [51, 60] +
[3] chrA [57, 66] +
[4] chrA [62, 71] +
[5] chrA [63, 72] +
... ... ... ...
[23] chrA [79, 88] -
[24] chrA [83, 92] -
[25] chrA [88, 97] -
[26] chrA [89, 98] -
[27] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)), param=readParam(dedup=TRUE))
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [51, 60] +
[2] chrA [57, 66] +
[3] chrA [62, 71] +
[4] chrA [63, 72] +
[5] chrA [76, 85] +
... ... ... ...
[15] chrA [79, 88] -
[16] chrA [79, 88] -
[17] chrA [88, 97] -
[18] chrA [89, 98] -
[19] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="both"))
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [50, 79] *
[2] chrB [90, 99] *
[3] chrB [99, 100] *
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="second"))
GRanges object with 4 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [75, 84] +
[2] chrB [90, 99] +
[3] chrB [70, 79] -
[4] chrB [99, 100] -
-------
seqinfo: 1 sequence from an unspecified genome
>
>
> proc.time()
user system elapsed
23.46 1.09 24.56
|
|
|
csaw.Rcheck/tests_x64/test-basic.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This is a testing stub that just provides a basic run-through of all the methods.
> # The real tests are located in inst/tests along with a Bash script for execution
> # and comparison. The separation into two folders is necessary to keep R CMD check
> # running with reasonable speed.
>
> suppressWarnings(suppressPackageStartupMessages(require(csaw)))
> both.files <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
> pe.file <- system.file("exdata", "pet.bam", package="csaw")
>
> # Checking data quality prior to counting.
> head(correlateReads(both.files))
[1] -0.0137654663 0.0005571408 0.0175021237 -0.0308470292 -0.0087488234
[6] -0.0120687468
> head(correlateReads(both.files, cross=FALSE))
[1] 1.0000000000 -0.0008601215 0.0170688852 -0.0475443596 0.0028128511
[6] -0.0030687197
>
> getPESizes(pe.file)
$sizes
[1] 70 90 20 150 10 30 10 2
$diagnostics
total.reads mapped.reads single mate.unmapped unoriented
23 23 3 0 1
inter.chr
1
>
> # Trying to count some single-end data.
> data <- windowCounts(both.files, ext=100)
> head(assay(data))
[,1] [,2]
[1,] 43 71
[2,] 57 89
[3,] 56 120
[4,] 53 141
[5,] 40 152
[6,] 59 135
> rowRanges(data)
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, width=500, spacing=200)
> head(assay(data))
[,1] [,2]
[1,] 204 455
[2,] 195 510
[3,] 186 483
[4,] 200 501
[5,] 187 468
[6,] 127 311
> rowRanges(data)
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 500] *
[2] chrA [201, 700] *
[3] chrA [401, 900] *
[4] chrA [601, 1100] *
[5] chrA [801, 1298] *
... ... ... ...
[15] chrC [ 401, 900] *
[16] chrC [ 601, 1100] *
[17] chrC [ 801, 1300] *
[18] chrC [1001, 1345] *
[19] chrC [1201, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> data$totals
[1] 1349 3291
>
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100))
> data$totals
[1] 914 2152
> data <- windowCounts(both.files, ext=100, param=readParam(dedup=TRUE))
> data$totals
[1] 1056 2582
> data <- windowCounts(both.files, ext=100, param=readParam(discard=GRanges("chrA", IRanges(50, 500))))
> data$totals
[1] 1186 2916
> data <- windowCounts(both.files, ext=100, param=readParam(restrict="chrA"))
> data$totals
[1] 451 1093
>
> # Trying to count some paired-end data.
> out <- windowCounts(pe.file, param=readParam(pe="both"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 2
[4,] 1
[5,] 4
[6,] 3
> out$totals
[1] 8
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="both", max.frag=100), width=100, filter=1L)
> assay(out)
[,1]
[1,] 2
[2,] 3
[3,] 1
[4,] 4
[5,] 3
> out$totals
[1] 7
> rowRanges(out)
GRanges object with 5 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrB [ 1, 100] *
[5] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
> out <- windowCounts(pe.file, param=readParam(pe="first"), width=100, filter=1L)
> assay(out)
[,1]
[1,] 3
[2,] 4
[3,] 4
[4,] 2
[5,] 6
[6,] 6
> out$totals
[1] 10
> rowRanges(out)
GRanges object with 6 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 100] *
[2] chrA [ 51, 150] *
[3] chrA [101, 200] *
[4] chrA [151, 200] *
[5] chrB [ 1, 100] *
[6] chrB [ 51, 100] *
-------
seqinfo: 2 sequences from an unspecified genome
>
> # Trying to convert it to a DGEList.
> asDGEList(data)
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 1
> asDGEList(data, lib.size=c(10, 10))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 10 1
Sample2 1 10 1
> asDGEList(data, norm=c(1,2))
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 451 1
Sample2 1 1093 2
>
> temp <- data
> temp$totals <- NULL
> asDGEList(temp) # Should spit out a warning.
An object of class "DGEList"
$counts
Sample1 Sample2
1 43 71
2 57 89
3 56 120
4 53 141
5 40 152
21 more rows ...
$samples
group lib.size norm.factors
Sample1 1 1293 1
Sample2 1 3142 1
Warning message:
In .local(object, ...) :
library sizes not found in 'totals', setting to NULL
>
> # Running some basic normalization.
> data <- windowCounts(both.files, ext=100, param=readParam(minq=100, dedup=TRUE))
>
> normOffsets(assay(data), lib.size=data$totals)
[1] 1.001197 0.998804
> normOffsets(assay(data), lib.size=data$totals, logratioTrim=.2)
[1] 1.003816 0.996199
> normOffsets(assay(data), lib.size=data$totals, method="RLE")
[1] 1.0037890 0.9962253
> normOffsets(data)
[1] 1.001197 0.998804
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
> normOffsets(data, logratioTrim=0.1)
[1] 1.0026764 0.9973307
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
> normOffsets(data, method="upperquartile")
[1] 0.9834651 1.0168129
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
>
> head(normOffsets(assay(data), lib.size=data$totals, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
> head(normOffsets(assay(data), lib.size=data$totals, type="loess", span=0.7))
[,1] [,2]
[1,] -0.4297765 0.4297765
[2,] -0.4391936 0.4391936
[3,] -0.3867962 0.3867962
[4,] -0.4215479 0.4215479
[5,] -0.3858107 0.3858107
[6,] -0.3915074 0.3915074
> head(normOffsets(data, type="loess"))
[,1] [,2]
[1,] -0.4047876 0.4047876
[2,] -0.4328410 0.4328410
[3,] -0.3864553 0.3864553
[4,] -0.4101296 0.4101296
[5,] -0.3788945 0.3788945
[6,] -0.3514597 0.3514597
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
> head(normOffsets(data, type="loess", span=0.5))
[,1] [,2]
[1,] -0.4120470 0.4120470
[2,] -0.4350054 0.4350054
[3,] -0.3740611 0.3740611
[4,] -0.4122536 0.4122536
[5,] -0.3722926 0.3722926
[6,] -0.3835921 0.3835921
Warning message:
'se.out=NULL' is deprecated.
Use 'se.out=TRUE' instead.
See help("Deprecated")
>
> # Assuming someone went around and pulled out some p-values for everybody.
> set.seed(128145-19238)
> nr <- nrow(data)
> tabled <- data.frame(logFC=rnorm(nr), logCPM=rnorm(nr), PValue=rbeta(nr, 1, 2))
> weighting <- rgamma(nr, 2, 1)
>
> mergeWindows(rowRanges(data), -1)
$id
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
[51] 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
$region
GRanges object with 71 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 100] *
[3] chrA [101, 150] *
[4] chrA [151, 200] *
[5] chrA [201, 250] *
... ... ... ...
[67] chrC [1101, 1150] *
[68] chrC [1151, 1200] *
[69] chrC [1201, 1250] *
[70] chrC [1251, 1300] *
[71] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100)
$id
[1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2
[39] 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
$region
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [1, 1298] *
[2] chrB [1, 870] *
[3] chrC [1, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> mergeWindows(rowRanges(data), 100, max.width=500)
$id
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 5 5 5
[39] 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8
$region
GRanges object with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 450] *
[2] chrA [451, 850] *
[3] chrA [851, 1298] *
[4] chrB [ 1, 450] *
[5] chrB [451, 870] *
[6] chrC [ 1, 450] *
[7] chrC [451, 900] *
[8] chrC [901, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
> merged <- mergeWindows(rowRanges(data), 100, sign=tabled$logFC > 0)
> merged
$id
[1] 1 2 2 3 4 4 4 5 5 6 7 8 9 9 9 9 10 10 11 12 13 14 15 15 15
[26] 15 16 17 18 18 18 18 18 19 19 20 21 22 23 24 24 25 25 26 27 28 29 29 30 30
[51] 31 31 31 31 32 33 34 34 34 34 35 36 37 37 38 39 40 41 41 42 43
$region
GRanges object with 43 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 1, 50] *
[2] chrA [ 51, 150] *
[3] chrA [151, 200] *
[4] chrA [201, 350] *
[5] chrA [351, 450] *
... ... ... ...
[39] chrC [1051, 1100] *
[40] chrC [1101, 1150] *
[41] chrC [1151, 1250] *
[42] chrC [1251, 1300] *
[43] chrC [1301, 1345] *
-------
seqinfo: 3 sequences from an unspecified genome
>
> head(combineTests(merged$id, tabled))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5047602 up
4 3 0 1 0.08956765 0.4125151 down
5 2 1 0 0.28172663 0.5047602 up
6 1 0 1 0.01949563 0.4125151 down
> head(combineTests(merged$id, tabled, weight=weighting))
nWindows logFC.up logFC.down PValue FDR direction
1 1 0 0 0.46328451 0.5622769 up
2 2 0 0 0.79272727 0.8116017 down
3 1 1 0 0.27967201 0.5228651 up
4 3 0 1 0.04669873 0.4255938 down
5 2 1 0 0.24536526 0.4795776 up
6 1 0 1 0.01949563 0.3373185 down
>
> head(getBestTest(merged$id, tabled))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 3 -0.24872062 -0.73322697 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5047602
4 5 -0.01753979 1.78172679 0.08956765 0.4442470
5 9 0.21512818 1.42847478 0.28172663 0.5047602
6 10 -1.10068046 -0.09313516 0.01949563 0.4442470
> head(getBestTest(merged$id, tabled, weight=weighting))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5783419
2 2 -0.41696325 1.60566251 1.00000000 1.0000000
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.04669873 0.4255938
5 9 0.21512818 1.42847478 0.24536526 0.4795776
6 10 -1.10068046 -0.09313516 0.01949563 0.3373185
> head(getBestTest(merged$id, tabled, by.pval=FALSE))
best logFC logCPM PValue FDR
1 1 0.21317827 0.53648572 0.46328451 0.5622769
2 2 -0.41696325 1.60566251 0.79272727 0.8116017
3 4 1.41995983 -0.91833741 0.27967201 0.5228651
4 5 -0.01753979 1.78172679 0.02985588 0.2567606
5 9 0.21512818 1.42847478 0.14086332 0.4038082
6 10 -1.10068046 -0.09313516 0.01949563 0.2567606
>
> # Pulling out some diagnostics.
> suppressPackageStartupMessages(require(org.Mm.eg.db))
> suppressPackageStartupMessages(require(TxDb.Mmusculus.UCSC.mm10.knownGene))
>
> current <- readRDS(system.file("exdata", "exrange.rds", package="csaw"))
> output <- detailRanges(current, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db)
> head(output$overlap)
[1] "Nrxn3|8|+" "" ""
[4] "1700007G11Rik|I|+" "Mannr|2|+" ""
> head(output$right)
[1] "Nrxn3|9|+[3846]" "Rprm|1|-[2293]" "" ""
[5] "" ""
> head(output$left)
[1] "" ""
[3] "" "1700007G11Rik|5|+[2890]"
[5] "" ""
>
> # Pulling out some reads.
> extractReads(both.files[1], GRanges("chrA", IRanges(100, 500)))
GRanges object with 143 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [ 94, 103] +
[2] chrA [106, 115] +
[3] chrA [120, 129] +
[4] chrA [120, 129] +
[5] chrA [129, 138] +
... ... ... ...
[139] chrA [467, 476] -
[140] chrA [482, 491] -
[141] chrA [490, 499] -
[142] chrA [491, 500] -
[143] chrA [499, 508] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)))
GRanges object with 27 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [43, 52] +
[2] chrA [51, 60] +
[3] chrA [57, 66] +
[4] chrA [62, 71] +
[5] chrA [63, 72] +
... ... ... ...
[23] chrA [79, 88] -
[24] chrA [83, 92] -
[25] chrA [88, 97] -
[26] chrA [89, 98] -
[27] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(both.files[1], GRanges("chrA", IRanges(50, 100)), param=readParam(dedup=TRUE))
GRanges object with 19 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrA [51, 60] +
[2] chrA [57, 66] +
[3] chrA [62, 71] +
[4] chrA [63, 72] +
[5] chrA [76, 85] +
... ... ... ...
[15] chrA [79, 88] -
[16] chrA [79, 88] -
[17] chrA [88, 97] -
[18] chrA [89, 98] -
[19] chrA [93, 102] -
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="both"))
GRanges object with 3 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [50, 79] *
[2] chrB [90, 99] *
[3] chrB [99, 100] *
-------
seqinfo: 1 sequence from an unspecified genome
> extractReads(pe.file, GRanges("chrB", IRanges(50, 100)), param=readParam(pe="second"))
GRanges object with 4 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chrB [75, 84] +
[2] chrB [90, 99] +
[3] chrB [70, 79] -
[4] chrB [99, 100] -
-------
seqinfo: 1 sequence from an unspecified genome
>
>
> proc.time()
user system elapsed
25.01 0.64 25.64
|
|
csaw.Rcheck/examples_i386/csaw-Ex.timings
|
csaw.Rcheck/examples_x64/csaw-Ex.timings
|