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/RtmpkztNNb/Rinst162aff4bb5a445/MMAPPR2data/extdata/wt.bam
## index: /tmp/RtmpkztNNb/Rinst162aff4bb5a445/MMAPPR2data/extdata/wt.bam.bai
## isOpen: FALSE 
## yieldSize: NA 
## obeyQname: FALSE 
## asMates: FALSE 
## qnamePrefixEnd: NA 
## qnameSuffixStart: NA
exampleMutBam()
## class: BamFile 
## path: /tmp/RtmpkztNNb/Rinst162aff4bb5a445/MMAPPR2data/extdata/mut.bam
## index: /tmp/RtmpkztNNb/Rinst162aff4bb5a445/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/RtmpkztNNb/Rinst162aff4bb5a445/MMAPPR2data/extdata/slc24a5.fa.gz"
goldenGFF()
## [1] "/tmp/RtmpkztNNb/Rinst162aff4bb5a445/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) (2022-10-25 r83175)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-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       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MMAPPR2data_1.13.0 BiocStyle_2.27.0  
## 
## loaded via a namespace (and not attached):
##  [1] crayon_1.5.2           cli_3.4.1              knitr_1.40            
##  [4] rlang_1.0.6            xfun_0.34              stringi_1.7.8         
##  [7] jsonlite_1.8.3         S4Vectors_0.37.0       RCurl_1.98-1.9        
## [10] Biostrings_2.67.0      htmltools_0.5.3        stats4_4.3.0          
## [13] sass_0.4.2             rmarkdown_2.17         evaluate_0.17         
## [16] jquerylib_0.1.4        bitops_1.0-7           fastmap_1.1.0         
## [19] GenomeInfoDb_1.35.0    IRanges_2.33.0         yaml_2.3.6            
## [22] bookdown_0.29          BiocManager_1.30.19    stringr_1.4.1         
## [25] compiler_4.3.0         codetools_0.2-18       XVector_0.39.0        
## [28] BiocParallel_1.33.0    digest_0.6.30          R6_2.5.1              
## [31] GenomeInfoDbData_1.2.9 parallel_4.3.0         GenomicRanges_1.51.0  
## [34] magrittr_2.0.3         bslib_0.4.0            tools_4.3.0           
## [37] Rsamtools_2.15.0       zlibbioc_1.45.0        BiocGenerics_0.45.0   
## [40] cachem_1.0.6

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