getBamFileList {easyRNASeq} | R Documentation |
A utility function to create a BamFileList-class
object from a set of filenames. The filenames need to contain the file path if they
are not in the working directory.
## S4 method for signature 'character,character' getBamFileList(filenames = character(0), indexnames = character(0))
filenames |
a character vector containing fully defined BAM file filenames |
indexnames |
a character vector containing fully defined BAM index file filenames |
# tutorial data - store the data in the BiocCache tdir <- tutorialData() # creating a BamFileList using a directory and pattern # using filenames (from the Bioc cache) filenames <- dir(tdir,pattern="[A,C,T,G]{6}\\.bam$",full.names=TRUE) indexnames <- sapply(paste0(sub(".*_","",basename(filenames)),".bai"),fetchData) bfl <- getBamFileList(filenames,indexnames) # get them recursively filenames <- dir(path=tdir,pattern="[A,C,T,G]{6}\\.bam$", full.names=TRUE,recursive=TRUE) indexnames <- sapply(paste0(sub(".*_","",basename(filenames)),".bai"),fetchData) bfl <- getBamFileList(filenames,indexnames)