Description Usage Arguments Details Author(s) Examples
View source: R/generate_posid.R
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.
1 2 3 | generate_posid(sites = NULL)
generate_posid(seqnames = NULL, strand = NULL, start = NULL, end = NULL, delim = "")
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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. |
generate_posid
generates a character vector of position IDs
Christopher Nobles, Ph.D.
1 2 3 4 5 6 7 8 9 10 | 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)
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