getContextSequences {cleanUpdTSeq} | R Documentation

## 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)

[Package cleanUpdTSeq version 1.30.0 Index]