cleanUpdTSeq (version 1.10.2)

getUpstreamSequence: Get upstream sequences of the putative pA site

Description

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

Usage

getUpstreamSequence(peaks, upstream = 40, genome)

Arguments

peaks

GRanges containing putative pA sites

upstream

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

genome

BSgenomeName

Value

Returns an object of GRanges with uptream 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 = getUpstreamSequence(peaks, upstream=40, genome=Drerio)