We first load the MMAPPR2data package:

library(MMAPPR2data, quietly = TRUE)
## Warning in fun(libname, pkgname): 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/RtmpVKkMBV/Rinst2f1d3416a68a5a/MMAPPR2data/extdata/wt.bam
## index: /tmp/RtmpVKkMBV/Rinst2f1d3416a68a5a/MMAPPR2data/extdata/wt.bam.bai
## isOpen: FALSE 
## yieldSize: NA 
## obeyQname: FALSE 
## asMates: FALSE 
## qnamePrefixEnd: NA 
## qnameSuffixStart: NA
exampleMutBam()
## class: BamFile 
## path: /tmp/RtmpVKkMBV/Rinst2f1d3416a68a5a/MMAPPR2data/extdata/mut.bam
## index: /tmp/RtmpVKkMBV/Rinst2f1d3416a68a5a/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/RtmpVKkMBV/Rinst2f1d3416a68a5a/MMAPPR2data/extdata/slc24a5.fa.gz"
goldenGFF()
## [1] "/tmp/RtmpVKkMBV/Rinst2f1d3416a68a5a/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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 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_1.18.0 BiocStyle_2.32.0  
## 
## loaded via a namespace (and not attached):
##  [1] crayon_1.5.2            httr_1.4.7              cli_3.6.2              
##  [4] knitr_1.46              rlang_1.1.3             xfun_0.43              
##  [7] UCSC.utils_1.0.0        jsonlite_1.8.8          S4Vectors_0.42.0       
## [10] Biostrings_2.72.0       htmltools_0.5.8.1       stats4_4.4.0           
## [13] sass_0.4.9              rmarkdown_2.26          evaluate_0.23          
## [16] jquerylib_0.1.4         bitops_1.0-7            fastmap_1.1.1          
## [19] GenomeInfoDb_1.40.0     IRanges_2.38.0          yaml_2.3.8             
## [22] lifecycle_1.0.4         bookdown_0.39           BiocManager_1.30.22    
## [25] compiler_4.4.0          codetools_0.2-20        XVector_0.44.0         
## [28] BiocParallel_1.38.0     digest_0.6.35           R6_2.5.1               
## [31] GenomeInfoDbData_1.2.12 parallel_4.4.0          GenomicRanges_1.56.0   
## [34] bslib_0.7.0             tools_4.4.0             Rsamtools_2.20.0       
## [37] zlibbioc_1.50.0         BiocGenerics_0.50.0     cachem_1.0.8

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