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/RtmpTpQ79O/Rinst26fae5794d93d9/MMAPPR2data/extdata/wt.bam
## index: /tmp/RtmpTpQ79O/Rinst26fae5794d93d9/MMAPPR2data/extdata/wt.bam.bai
## isOpen: FALSE 
## yieldSize: NA 
## obeyQname: FALSE 
## asMates: FALSE 
## qnamePrefixEnd: NA 
## qnameSuffixStart: NA
exampleMutBam()
## class: BamFile 
## path: /tmp/RtmpTpQ79O/Rinst26fae5794d93d9/MMAPPR2data/extdata/mut.bam
## index: /tmp/RtmpTpQ79O/Rinst26fae5794d93d9/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/RtmpTpQ79O/Rinst26fae5794d93d9/MMAPPR2data/extdata/slc24a5.fa.gz"
goldenGFF()
## [1] "/tmp/RtmpTpQ79O/Rinst26fae5794d93d9/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 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-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_1.6.0 BiocStyle_2.20.0 
## 
## loaded via a namespace (and not attached):
##  [1] XVector_0.32.0         knitr_1.33             magrittr_2.0.1        
##  [4] GenomicRanges_1.44.0   IRanges_2.26.0         BiocGenerics_0.38.0   
##  [7] zlibbioc_1.38.0        BiocParallel_1.26.0    R6_2.5.0              
## [10] rlang_0.4.11           GenomeInfoDb_1.28.0    stringr_1.4.0         
## [13] tools_4.1.0            parallel_4.1.0         xfun_0.23             
## [16] jquerylib_0.1.4        htmltools_0.5.1.1      yaml_2.2.1            
## [19] digest_0.6.27          crayon_1.4.1           bookdown_0.22         
## [22] GenomeInfoDbData_1.2.6 BiocManager_1.30.15    S4Vectors_0.30.0      
## [25] sass_0.4.0             bitops_1.0-7           RCurl_1.98-1.3        
## [28] evaluate_0.14          rmarkdown_2.8          stringi_1.6.2         
## [31] compiler_4.1.0         bslib_0.2.5.1          Biostrings_2.60.0     
## [34] Rsamtools_2.8.0        stats4_4.1.0           jsonlite_1.7.2

Thanks to Mike Love’s alpineData package for vignette structure inspiration.