To install chromhmmData use
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("chromhmmData")This package include the genomic annotations required for running ChromHMM.
This includes:
CHROMSIZES: text files with the chromosomes’ sizesCOORDS: bed files with the coordinates of different genomic featuresANCHORFILES: text files with transcription start and end sites of known genesThe annotations for four different genomes are included in the package. Those are the human hg18 and hg19 and the mouse mm10 and mm9.
Use system.file to access the files and directorys. For example
# access a directory
chromsizes <- system.file('extdata/CHROMSIZES', package = 'chromhmmData')
dir(chromsizes)
#> [1] "hg18.txt" "hg19.txt" "mm10.txt" "mm9.txt"
# access a file
system.file('extdata/CHROMSIZES', 'hg19.txt', package = 'chromhmmData')
#> [1] "/private/var/folders/sk/hy088prx12l_cqspv3lbpl9s6_3r11/T/RtmpfrF1ah/Rinst48a77110e7d/chromhmmData/extdata/CHROMSIZES/hg19.txt"These annotation files are obtained from ChromHMM source code repository.
sessionInfo()
#> R version 4.1.0 Patched (2021-05-24 r80367)
#> Platform: x86_64-apple-darwin17.7.0 (64-bit)
#> Running under: macOS High Sierra 10.13.6
#>
#> Matrix products: default
#> BLAS: /Users/ka36530_ca/R-stuff/bin/R-4-1/lib/libRblas.dylib
#> LAPACK: /Users/ka36530_ca/R-stuff/bin/R-4-1/lib/libRlapack.dylib
#>
#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] chromhmmData_0.99.2
#>
#> loaded via a namespace (and not attached):
#> [1] digest_0.6.27 R6_2.5.0 jsonlite_1.7.2 magrittr_2.0.1
#> [5] evaluate_0.14 rlang_0.4.11 stringi_1.6.2 jquerylib_0.1.4
#> [9] bslib_0.2.5.1 rmarkdown_2.9 tools_4.1.0 stringr_1.4.0
#> [13] xfun_0.24 yaml_2.2.1 compiler_4.1.0 htmltools_0.5.1.1
#> [17] knitr_1.33 sass_0.4.0