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/RtmpJFEyX2/Rinst2ed2dc56970f3c/MMAPPR2data/extdata/wt.bam
## index: /tmp/RtmpJFEyX2/Rinst2ed2dc56970f3c/MMAPPR2data/extdata/wt.bam.bai
## isOpen: FALSE 
## yieldSize: NA 
## obeyQname: FALSE 
## asMates: FALSE 
## qnamePrefixEnd: NA 
## qnameSuffixStart: NA
exampleMutBam()
## class: BamFile 
## path: /tmp/RtmpJFEyX2/Rinst2ed2dc56970f3c/MMAPPR2data/extdata/mut.bam
## index: /tmp/RtmpJFEyX2/Rinst2ed2dc56970f3c/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/RtmpJFEyX2/Rinst2ed2dc56970f3c/MMAPPR2data/extdata/slc24a5.fa.gz"
goldenGFF()
## [1] "/tmp/RtmpJFEyX2/Rinst2ed2dc56970f3c/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 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              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_1.12.0 BiocStyle_2.26.0  
## 
## loaded via a namespace (and not attached):
##  [1] bslib_0.4.0            compiler_4.2.1         BiocManager_1.30.19   
##  [4] jquerylib_0.1.4        GenomeInfoDb_1.34.0    XVector_0.38.0        
##  [7] bitops_1.0-7           tools_4.2.1            zlibbioc_1.44.0       
## [10] digest_0.6.30          jsonlite_1.8.3         evaluate_0.17         
## [13] rlang_1.0.6            cli_3.4.1              yaml_2.3.6            
## [16] parallel_4.2.1         xfun_0.34              fastmap_1.1.0         
## [19] GenomeInfoDbData_1.2.9 stringr_1.4.1          knitr_1.40            
## [22] Biostrings_2.66.0      sass_0.4.2             S4Vectors_0.36.0      
## [25] IRanges_2.32.0         stats4_4.2.1           R6_2.5.1              
## [28] BiocParallel_1.32.0    rmarkdown_2.17         bookdown_0.29         
## [31] magrittr_2.0.3         Rsamtools_2.14.0       codetools_0.2-18      
## [34] htmltools_0.5.3        BiocGenerics_0.44.0    GenomicRanges_1.50.0  
## [37] stringi_1.7.8          RCurl_1.98-1.9         cachem_1.0.6          
## [40] crayon_1.5.2

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