getContextSequences: Retrieve upstream and downstream sequences

In jianhong/cleanUpdTSeq: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

Retrieve upstream and downstream sequences

Description

Retrieve upstream and downstream sequences of pA sites from a BSgenome object based on a GRanges object

Usage

getContextSequences(peaks, upstream = 40L, downstream = 30L, genome)

Arguments

peaks	An object of GRanges representing pA sites
upstream	An integer(1) vector, length of upstream sequence of pA sites, including pA site.
downstream	An integer(1) vector, length of downstream sequences of pA sites
genome	An object of BSgenome.

Value

A data.frame containing sequences upstream and downstream pA sites:

upstream.seq

sequence upstream pA site, including pA site

downstream.seq

sequence downstream pA site

Author(s)

Haibo Liu

Examples

library(BSgenome.Drerio.UCSC.danRer7)
testFile <- system.file("extdata", "test.bed",
                        package = "cleanUpdTSeq")
peaks <- BED6WithSeq2GRangesSeq(file = testFile, 
                               skip = 1L, withSeq = FALSE)
peaks_seq <- getContextSequences(peaks, 
                                 upstream = 40L, 
                                 downstream = 30L,
                                 genome = Drerio) 
                                                        

jianhong/cleanUpdTSeq documentation built on Nov. 5, 2024, 7:46 a.m.