getBamFileList {easyRNASeq} | R Documentation |
A utility function to create a linkS4class{BamFileList-class}
BamFileList
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' getBamFileList(filenames = character(0))
filenames |
a character vector containing fully defined filenames |
a linkS4class{BamFileList-class}
BamFileList
linkS4class{BamFileList-class}
BamFileList
dir
library(curl) # get the example data files - we retrieve a set of example bam files # from GitHub using curl, as well as their index. invisible(sapply(c("ACACTG","ACTAGC"),function(bam){ curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/", "master/tutorial/easyRNASeq/",bam,".bam"),paste0(bam,".bam")) curl_download(paste0("https://github.com/UPSCb/UPSCb/raw/", "master/tutorial/easyRNASeq/",bam,".bam.bai"),paste0(bam,".bam.bai")) })) # creating a BamFileList using a directory and pattern bfl <- getBamFileList(dir(".",pattern="[A,C,T,G]{6}\\.bam$", full.names=TRUE)) # using filenames filenames <- dir(".",pattern="[A,C,T,G]{6}\\.bam$",full.names=TRUE) bfl <- getBamFileList(filenames) # get them recursively filenames <- dir(path=".",pattern="[A,C,T,G]{6}\\.bam$", full.names=TRUE,recursive=TRUE) bfl <- getBamFileList(filenames)