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/Rtmpxwnh05/Rinst599f66e820c9/MMAPPR2data/extdata/wt.bam
## index: /tmp/Rtmpxwnh05/Rinst599f66e820c9/MMAPPR2data/extdata/wt.bam.bai
## isOpen: FALSE 
## yieldSize: NA 
## obeyQname: FALSE 
## asMates: FALSE 
## qnamePrefixEnd: NA 
## qnameSuffixStart: NA
exampleMutBam()
## class: BamFile 
## path: /tmp/Rtmpxwnh05/Rinst599f66e820c9/MMAPPR2data/extdata/mut.bam
## index: /tmp/Rtmpxwnh05/Rinst599f66e820c9/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/Rtmpxwnh05/Rinst599f66e820c9/MMAPPR2data/extdata/slc24a5.fa.gz"
goldenGFF()
## [1] "/tmp/Rtmpxwnh05/Rinst599f66e820c9/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) (2019-10-24 r77329)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.3 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_1.1.0 BiocStyle_2.15.0 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.2             XVector_0.27.0         knitr_1.25            
##  [4] magrittr_1.5           GenomicRanges_1.39.1   BiocGenerics_0.33.0   
##  [7] zlibbioc_1.33.0        IRanges_2.21.1         BiocParallel_1.21.0   
## [10] rlang_0.4.1            stringr_1.4.0          GenomeInfoDb_1.23.0   
## [13] tools_4.0.0            parallel_4.0.0         xfun_0.10             
## [16] htmltools_0.4.0        yaml_2.2.0             digest_0.6.22         
## [19] bookdown_0.14          GenomeInfoDbData_1.2.2 BiocManager_1.30.9    
## [22] S4Vectors_0.25.0       bitops_1.0-6           RCurl_1.95-4.12       
## [25] evaluate_0.14          rmarkdown_1.16         stringi_1.4.3         
## [28] compiler_4.0.0         Biostrings_2.55.0      Rsamtools_2.3.0       
## [31] stats4_4.0.0

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