getUpstreamSequence: Get upstream sequences of the putative pA site

Description Usage Arguments Value Author(s) Examples

View source: R/getUpstreamSequence.R

Description

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

Usage

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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

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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)

jianhong/cleanUpdTSeq documentation built on Nov. 6, 2019, 9:56 a.m.