readTranscriptFeatures {genomation} | R Documentation |
Function for reading exon intron and promoter structure from a given bed file
readTranscriptFeatures(location,remove.unusual=TRUE, up.flank=1000,down.flank=1000,unique.prom=TRUE) ## S4 method for signature 'character' readTranscriptFeatures(location, remove.unusual = TRUE, up.flank = 1000, down.flank = 1000, unique.prom = TRUE)
location |
location of the bed file with 12 or more columns.
The file can end in |
remove.unusual |
remove the chromomesomes with unsual names, mainly random chromsomes etc |
up.flank |
up-stream from TSS to detect promoter boundaries |
down.flank |
down-stream from TSS to detect promoter boundaries |
unique.prom |
get only the unique promoters, promoter boundaries will not have a gene name if you set this option to be TRUE |
a GRangesList
containing locations of exon/intron/promoter/TSS
one bed track per file is only accepted, the bed files with multiple tracks will cause en error
my.bed12.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation") my.bed12.file feats = readTranscriptFeatures(my.bed12.file) names(feats) sapply(feats, head)