getDownstreamSequence {cleanUpdTSeq}R Documentation

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.

Author(s)

Sarah Sheppard, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu

Examples

library(BSgenome.Drerio.UCSC.danRer7)
        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)

[Package cleanUpdTSeq version 1.22.0 Index]