getDownstreamSequence {cleanUpdTSeq} | R Documentation |
This function gets the sequence upstream of a putative pA site (including the site)
getDownstreamSequence(peaks, downstream = 20, genome)
peaks |
GRanges containing putative pA sites |
downstream |
downstream = int. This is the length of the sequence to get. |
genome |
BSgenomeName |
Returns an object of GRanges with downtream sequences.
Sarah Sheppard, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu
testFile <- system.file("extdata", "test.bed", package="cleanUpdTSeq") testSet <- read.table(testFile, sep="\t", header=TRUE) peaks <- BED2GRangesSeq(testSet[1:10, ], withSeq=FALSE) seq = getDownstreamSequence(peaks, downstream=30, genome=Drerio)