getUpstreamSequence: Get upstream sequences of the putative pA site

In cleanUpdTSeq: This package classifies putative polyadenylation sites as true or false/internally oligodT primed

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.

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 = getUpstreamSequence(peaks, upstream=40, genome=Drerio)

cleanUpdTSeq documentation built on Nov. 8, 2020, 8:30 p.m.