BED6WithSeq2GRangesSeq: Covert (extended) BED6 file to a GRanges object

In haibol2016/cleanUpdTSeq: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

Covert (extended) BED6 file to a GRanges object

Description

Convert to a GRanges object from a (extended) BED6 file with at least six columns: chrom, chromStart, strEnd, name, score and strand, and optional upstream sequences (including pA sites) and downstream sequences of pA sites

Usage

BED6WithSeq2GRangesSeq(
  file,
  skip = 1L,
  withSeq = TRUE,
  upstream.seq.ind = 7L,
  downstream.seq.ind = 8L
)

Arguments

file	A character(1) vector, representing a path to a extended BED file containing at least six columns in the order of chrom, chromStart, strEnd, name, score and strand. The strand information must be designated as "+", or "-". Optional fields–upstream sequences (including pA sites) and downstream sequences of pA sites–are allowed. For more details about the BED format, see https://genome.ucsc.edu/FAQ/FAQformat.html#format1.
skip	A integer(1) vector, indicating how many rows (header lines) to skip when the BED file is read into R.
withSeq	A logical(1) vector, indicating that upstream and downstream sequences flanking pA sites are included in the file
upstream.seq.ind	An integer(1),vector delineating the column location of upstream sequences of the putative pA site
downstream.seq.ind	An integer(1),vector delineating the column location of downstream sequences of the putative pA site

Value

An object of GRanges

Author(s)

Haibo Liu, Lihua J. Zhu

Examples

testFile <- system.file("extdata", "test.bed",
                        package = "cleanUpdTSeq")
peaks <- BED6WithSeq2GRangesSeq(file = testFile, 
                               skip = 1L, withSeq = TRUE)

haibol2016/cleanUpdTSeq documentation built on April 14, 2022, 9:56 p.m.