Instructions on loading BAM files and indices in MMAPPR2data package.
MMAPPR2data 1.4.0
We first load the MMAPPR2data
package:
library(MMAPPR2data, quietly = TRUE)
This package contains the following two functions, which
provide easy access to the BAM files and their indices,
returning BamFile
objects:
exampleWTbam()
## class: BamFile
## path: /tmp/Rtmp56aMqf/Rinst1b987505cc04/MMAPPR2data/extdata/wt.bam
## index: /tmp/Rtmp56aMqf/Rinst1b987505cc04/MMAPPR2data/extdata/wt.bam.bai
## isOpen: FALSE
## yieldSize: NA
## obeyQname: FALSE
## asMates: FALSE
## qnamePrefixEnd: NA
## qnameSuffixStart: NA
exampleMutBam()
## class: BamFile
## path: /tmp/Rtmp56aMqf/Rinst1b987505cc04/MMAPPR2data/extdata/mut.bam
## index: /tmp/Rtmp56aMqf/Rinst1b987505cc04/MMAPPR2data/extdata/mut.bam.bai
## isOpen: FALSE
## yieldSize: NA
## obeyQname: FALSE
## asMates: FALSE
## qnamePrefixEnd: NA
## qnameSuffixStart: NA
Annotation data for the region is also included with the package and can be accessed with these two functions:
goldenFasta()
## [1] "/tmp/Rtmp56aMqf/Rinst1b987505cc04/MMAPPR2data/extdata/slc24a5.fa.gz"
goldenGFF()
## [1] "/tmp/Rtmp56aMqf/Rinst1b987505cc04/MMAPPR2data/extdata/slc24a5.gff.gz"
For details on the source of these files, and on their construction
see ?MMAPPR2data
and the inst/scripts/
folder.
sessionInfo()
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.12-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] MMAPPR2data_1.4.0 BiocStyle_2.18.0
##
## loaded via a namespace (and not attached):
## [1] XVector_0.30.0 knitr_1.30 magrittr_1.5
## [4] GenomicRanges_1.42.0 BiocGenerics_0.36.0 zlibbioc_1.36.0
## [7] IRanges_2.24.0 BiocParallel_1.24.0 rlang_0.4.8
## [10] stringr_1.4.0 GenomeInfoDb_1.26.0 tools_4.0.3
## [13] parallel_4.0.3 xfun_0.18 htmltools_0.5.0
## [16] yaml_2.2.1 digest_0.6.27 crayon_1.3.4
## [19] bookdown_0.21 GenomeInfoDbData_1.2.4 BiocManager_1.30.10
## [22] S4Vectors_0.28.0 bitops_1.0-6 RCurl_1.98-1.2
## [25] evaluate_0.14 rmarkdown_2.5 stringi_1.5.3
## [28] compiler_4.0.3 Biostrings_2.58.0 Rsamtools_2.6.0
## [31] stats4_4.0.3
Thanks to Mike Love’s alpineData package for vignette structure inspiration.