generate_posid: Generate position IDs.

Description Usage Arguments Details Author(s) Examples

View source: R/generate_posid.R

Description

Given a set of genomic integration positions, the function generates a character vector of integrated positions in the following format: chr(+/-)pos, where chr is the chromosome, (+/-) designates the orientation of the integration, and pos is the position of the integrated element.

Usage

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generate_posid(sites = NULL)

generate_posid(seqnames = NULL, strand = NULL, start = NULL, end = NULL, delim = "")

Arguments

sites

a GRanges object where each row represents one integrated element.

seqnames

a character vector of chromosomes for integrated elements, i.e. chr1, chr3, chrX.

strand

orientation or strand on which the integrated element is on (+, -, *)

start

the lower numerical position of the integrated element, considered the start for "+" integrated elements.

end

the greater numerical position of the integrated element, considered the end for "+" integrated elements.

delim

a single character to delimit the data within the string.

Details

generate_posid generates a character vector of position IDs

Author(s)

Christopher Nobles, Ph.D.

Examples

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chr <- c("chr1", "chr3", "chrX")
strands <- c("+", "-", "+")
starts <- c(900231, 13254892, 603292)
ends <- c(900431, 13255292, 603592)
ranges <- IRanges(start = starts, end = ends)
gr <- GRanges(seqnames = chr, ranges = ranges, strand = strands)

generate_posid(sites = gr)

generate_posid(seqnames = chr, strand = strands, start = starts, end = ends)

cnobles/gintools documentation built on Aug. 22, 2019, 10:36 a.m.