cleanUpdTSeq (version 1.10.2)

getDownstreamSequence: getDownstreamSequence

Description

This function gets the sequence upstream of a putative pA site (including the site)

Usage

getDownstreamSequence(peaks, downstream = 20, genome)

Arguments

peaks

GRanges containing putative pA sites

downstream

downstream = int. This is the length of the sequence to get.

genome

BSgenomeName

Value

Returns an object of GRanges with downtream sequences.

Examples

        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)