We first load the MMAPPR2data package:

library(MMAPPR2data, quietly = TRUE)
## Warning: Package 'MMAPPR2data' is deprecated and will be removed from
##   Bioconductor version 3.20

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/RtmpRFGxLY/Rinst1951aa3725aab7/MMAPPR2data/extdata/wt.bam
## index: /tmp/RtmpRFGxLY/Rinst1951aa3725aab7/MMAPPR2data/extdata/wt.bam.bai
## isOpen: FALSE 
## yieldSize: NA 
## obeyQname: FALSE 
## asMates: FALSE 
## qnamePrefixEnd: NA 
## qnameSuffixStart: NA
exampleMutBam()
## class: BamFile 
## path: /tmp/RtmpRFGxLY/Rinst1951aa3725aab7/MMAPPR2data/extdata/mut.bam
## index: /tmp/RtmpRFGxLY/Rinst1951aa3725aab7/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/RtmpRFGxLY/Rinst1951aa3725aab7/MMAPPR2data/extdata/slc24a5.fa.gz"
goldenGFF()
## [1] "/tmp/RtmpRFGxLY/Rinst1951aa3725aab7/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 Under development (unstable) (2023-11-11 r85510)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## 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       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MMAPPR2data_1.17.1 BiocStyle_2.31.0  
## 
## loaded via a namespace (and not attached):
##  [1] crayon_1.5.2            cli_3.6.1               knitr_1.45             
##  [4] rlang_1.1.2             xfun_0.41               jsonlite_1.8.7         
##  [7] S4Vectors_0.41.1        RCurl_1.98-1.13         Biostrings_2.71.1      
## [10] htmltools_0.5.7         stats4_4.4.0            sass_0.4.7             
## [13] rmarkdown_2.25          evaluate_0.23           jquerylib_0.1.4        
## [16] bitops_1.0-7            fastmap_1.1.1           GenomeInfoDb_1.39.1    
## [19] IRanges_2.37.0          yaml_2.3.7              bookdown_0.36          
## [22] BiocManager_1.30.22     compiler_4.4.0          codetools_0.2-19       
## [25] XVector_0.43.0          BiocParallel_1.37.0     digest_0.6.33          
## [28] R6_2.5.1                GenomeInfoDbData_1.2.11 parallel_4.4.0         
## [31] GenomicRanges_1.55.1    bslib_0.5.1             tools_4.4.0            
## [34] Rsamtools_2.19.2        zlibbioc_1.49.0         BiocGenerics_0.49.1    
## [37] cachem_1.0.8

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