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CHECK report for csaw on veracruz1

This page was generated on 2018-04-12 13:39:39 -0400 (Thu, 12 Apr 2018).

Package 314/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.12.0
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)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: csaw
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings csaw_1.12.0.tar.gz
StartedAt: 2018-04-12 02:23:10 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:29:10 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 359.3 seconds
RetCode: 0
Status:  OK 
CheckDir: csaw.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings csaw_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/csaw.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
detailRanges 12.257  0.497  12.926
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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") 
 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: OK


Installation output

csaw.Rcheck/00install.out

* installing *source* package ‘csaw’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c annotator.cpp -o annotator.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c bam_utils.cpp -o bam_utils.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c best_in_cluster.cpp -o best_in_cluster.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c check_bimodality.cpp -o check_bimodality.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c correlate_reads.cpp -o correlate_reads.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c find_maxima.cpp -o find_maxima.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_cluster_stats.cpp -o get_cluster_stats.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_profile.cpp -o get_profile.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_rle_counts.cpp -o get_rle_counts.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c init.cpp -o init.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c merge_windows.cpp -o merge_windows.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c pair_reads.cpp -o pair_reads.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c single_reads.cpp -o single_reads.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o csaw.so 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 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/lib/libhts.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.6-bioc/meat/csaw.Rcheck/csaw/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (csaw)

Tests output

csaw.Rcheck/tests/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-apple-darwin15.6.0 (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 
 21.942   0.657  22.900 

csaw.Rcheck/tests/test-basic.Rout.save


R Under development (unstable) (2016-10-17 r71531) -- "Unsuffered Consequences"
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> # 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 

Example timings

csaw.Rcheck/csaw-Ex.timings

nameusersystemelapsed
SEmethods1.3690.0241.407
checkBimodality0.6110.0070.627
clusterFDR0.9210.0020.931
clusterWindows2.2830.0062.324
combineTests0.0750.0010.078
consolidateClusters3.3980.0093.456
consolidateSizes1.1040.0081.124
correlateReads0.2420.0030.245
csawUsersGuide0.0020.0000.002
detailRanges12.257 0.49712.926
empiricalFDR0.0060.0000.008
extractReads0.8860.0240.924
filterWindows0.6310.0060.646
findMaxima0.1820.0030.193
getBestTest0.0430.0010.046
getPESizes0.2360.0010.239
getWidths0.4220.0050.430
maximizeCcf0.0020.0000.002
mergeWindows0.0470.0010.049
mixedClusters0.0160.0000.016
normOffsets0.3470.0040.356
overlapStats0.2260.0030.230
profileSites0.6290.0060.644
readParam0.0520.0000.052
regionCounts0.3300.0030.342
scaledAverage0.4420.0040.449
strandedCounts1.4430.0151.485
upweightSummit0.0060.0010.007
windowCounts0.6840.0060.692
wwhm0.0970.0010.098