loadCopyNumberCallsCNVkit: loadCopyNumberCallsCNVkit

In bernatgel/CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

loadCopyNumberCallsCNVkit

Description

Loads copy number calls from CNVkit.cns file format

Usage

loadCopyNumberCallsCNVkit(cnvkit.file, chr.col = "chromosome", start.col = "start", end.col = "end", segment.value.col = "log2", file.type = "auto", cn.col = NULL, zero.based = TRUE, genome = NULL, verbose = TRUE)

Arguments

cnvkit.file	The name of the file with the data
chr.col	(number or character) The name or number of the column with chromosome information. If NULL, it is automatically identified. (defaults to "chromosome")
start.col	(number or character) The name or number of the column with start position information. If NULL, it is automatically identified. (defaults to "start")
end.col	(number or character) The name or number of the column with end position information. If NULL, it is automatically identified. (defaults to "end")
segment.value.col	(number or character) The name or number of the column with segment value. If NULL, it is automatically identified. (defaults to "log2")
file.type	(character) wheter to load ".cns", ".cnr" or "auto" if the file type is automatically recognised. (defaults to "auto)
cn.col	(number or character) The name or number of the column with CN information. If NULL, it is automatically identified. (defaults to NULL)
zero.based	(logical) Whether the data is zero-based and half open (i.e. ranges are defined by (start:end] so chr1:10-20 represents nine bases long features spanning from base 11 to 20). (defaults to FALSE)
genome	(character) The name of the genome (defaults to NULL)
verbose	(logical) Whether to show information messages. (defaults to TRUE)

Details

This function will load segments data from CNVkit.cns file format and from CNVkit.cnr. Internally it uses the toGRanges function from regioneR package and can work with any format accepted by it, including R objects and local or remote files. If no column names are specified, it will use simple heuristics to try to identify the relevant data columns.

Value

A GRanges with a range per copy number segment.

Examples

## loadCopyNumberCallsCNVkit from .cns file format:
## An example of .cns file format is found at https://github.com/etal/cnvkit/blob/master/test/formats/cl_seq.cns.

# Loading a CNVkit.cns file 
cnvkit.file <- system.file("extdata", "CNVkit_output.cns", package = "CopyNumberPlots", mustWork = TRUE)
cnv.call <- loadCopyNumberCallsCNVkit(cnvkit.file)

# Loading a CNVkit.cnr file
cnvkit.file <- system.file("extdata", "CNVkit_output.cnr", package = "CopyNumberPlots", mustWork = TRUE)
cnv.call <- loadCopyNumberCallsCNVkit(cnvkit.file)

bernatgel/CopyNumberPlots documentation built on Sept. 22, 2023, 1:53 a.m.