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/RtmpZxxifV/Rinst63b96af89db5/MMAPPR2data/extdata/wt.bam
## index: /tmp/RtmpZxxifV/Rinst63b96af89db5/MMAPPR2data/extdata/wt.bam.bai
## isOpen: FALSE 
## yieldSize: NA 
## obeyQname: FALSE 
## asMates: FALSE 
## qnamePrefixEnd: NA 
## qnameSuffixStart: NA
exampleMutBam()
## class: BamFile 
## path: /tmp/RtmpZxxifV/Rinst63b96af89db5/MMAPPR2data/extdata/mut.bam
## index: /tmp/RtmpZxxifV/Rinst63b96af89db5/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/RtmpZxxifV/Rinst63b96af89db5/MMAPPR2data/extdata/slc24a5.fa.gz"
goldenGFF()
## [1] "/tmp/RtmpZxxifV/Rinst63b96af89db5/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 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.11-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.11-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_1.2.0 BiocStyle_2.16.0 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.4.6           XVector_0.28.0         knitr_1.28            
##  [4] magrittr_1.5           GenomicRanges_1.40.0   BiocGenerics_0.34.0   
##  [7] zlibbioc_1.34.0        IRanges_2.22.1         BiocParallel_1.22.0   
## [10] rlang_0.4.6            stringr_1.4.0          GenomeInfoDb_1.24.0   
## [13] tools_4.0.0            parallel_4.0.0         xfun_0.13             
## [16] htmltools_0.4.0        yaml_2.2.1             digest_0.6.25         
## [19] crayon_1.3.4           bookdown_0.18          GenomeInfoDbData_1.2.3
## [22] BiocManager_1.30.10    S4Vectors_0.26.0       bitops_1.0-6          
## [25] RCurl_1.98-1.2         evaluate_0.14          rmarkdown_2.1         
## [28] stringi_1.4.6          compiler_4.0.0         Biostrings_2.56.0     
## [31] Rsamtools_2.4.0        stats4_4.0.0

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