transformChr: transformChr

In CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

Description

Transformation of the chromosomes

Usage

transformChr(chr, chr.transformation = "23:X,24:Y,25:MT")

Arguments

chr	(character) The chromosome names to transform
chr.transformation	(character) The transformation of the chromosomes names in a comma separated "key:value" format.(defaults to "23:X,24:Y,25:MT")

Details

This function will transform the name of the chormosomes, according to the parameter chr.transformation. This is useful in situations were files, such as .seg files as the ones generated by CNVkit, have the chromosome names as numbers. In order to transform the sexual and mitocondrial chromosomes from numbers back to characters, we can use this function. The exact transformation might be provided as described at https://cnvkit.readthedocs.io/en/stable/importexport.html#import-seg, (e.g. "key:value")

Value

A character vector where the name of the chromosomes have been changed according to chr.transformation parameter.

Examples

seg.file <- system.file("extdata", "DNACopy_output.seg", package = "CopyNumberPlots", mustWork = TRUE)
seg.data <- read.table(file = seg.file, sep = "\t", skip = 1, stringsAsFactors = FALSE)
colnames(seg.data) <-  c("ID", "chrom", "loc.start", "loc.end", "num.mark", "seg.mean")

# here we have the name of the chromosomes in a number format and how many segments are in each one.
table(seg.data$chrom)

# by this way we have the name 23 and 24 respectively transformed to X and Y.
seg.data$chrom <- transformChr(chr = seg.data$chrom, chr.transformation ="23:X,24:Y,25:MT")
table(seg.data$chrom)

CopyNumberPlots documentation built on Nov. 8, 2020, 6:51 p.m.