loadCopyNumberCallsCnmops: loadCopyNumberCallsCnmops

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

loadCopyNumberCallsCnmops

Description

Loads copy number calls from either cn.mops result class or in a tabular format

Usage

loadCopyNumberCallsCnmops(cn.mops.res, chr.col = NULL, start.col = NULL, end.col = NULL, cn.col = "CN", segment.value.col = "median", genome = NULL, verbose = TRUE)

Arguments

cn.mops.res	The name of the file with the data or the name of the variable 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 NULL)
start.col	(number or character) The name or number of the column with start position information. If NULL, it is automatically identified. (defaults to NULL)
end.col	(number or character) The name or number of the column with end position information. If NULL, it is automatically identified. (defaults to NULL)
cn.col	(number or character) The name or number of the column with CN information. If NULL, it is automatically identified. (defaults to "CN")
segment.value.col	(number or character) The name or number of the column with segment value. It can be mean or median. If NULL, it is automatically identified. (defaults to "median")
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 either cn.mops result class or in a tabular format from a file. 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. Column names of the format loaded are specified as default but, 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 or a list of GRanges with a GRanges per sample.

Examples

# loadCopyNumberCallsCnmops from cn.mops result class:
#NOT RUN - Example loading data from a results object created by cn.mops
# require(cn.mops)
# data(cn.mops, package = "cn.mops")

# cn.mops.res <- cn.mops(XRanges)
# cn.mops.res <- calcIntegerCopyNumbers(cn.mops.res)
# cnv.call <- loadCopyNumberCallsCnmops(cn.mops.res = cn.mops.res)  

# loadCopyNumberCallsCnmops from a file where cn.mops result was saved:
cn.mops.res <- system.file("extdata", "cn.mops.segmentation.csv", package = "CopyNumberPlots", mustWork = TRUE)
cnv.call <- loadCopyNumberCallsCnmops(cn.mops.res = cn.mops.res) 

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