getUpstreamSequence {cleanUpdTSeq} | R Documentation

## 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.

### 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)

[Package cleanUpdTSeq version 1.22.2 Index]