loadCopyNumberCallsSeg {CopyNumberPlots} | R Documentation

## loadCopyNumberCallsSeg

### Description

Loads copy number calls from .seg file format

### Usage

    loadCopyNumberCallsSeg (seg.file, chr.col = "chrom", start.col = "loc.start", end.col = "loc.end", segment.value.col = "seg.mean", cn.col = NULL, genome = NULL, chr.transformation = "23:X,24:Y,25:MT", verbose = TRUE)

### Arguments

`seg.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 "chrom")
`start.col` | (number or character) The name or number of the column with start position information. If NULL, it is automatically identified. (defaults to "loc.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 "loc.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 "seg.mean")
`cn.col` | (number or character)The name or number of the column with CN information. If NULL, it is automatically identified. (defaults to NULL)
`genome` | (character) The name of the genome (defaults to NULL)
`chr.transformation` | (character)(character) The transformation of the chromosome names in a comma separated "key:value" format as detailed at https://cnvkit.readthedocs.io/en/stable/importexport.html#import-seg.(defaults to "23:X,24:Y,25:MT")
`verbose` | (logical) Whether to show information messages. (defaults to TRUE)

### Details

This function will load segments data from .seg file format. 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

    ## loadCopyNumberCallsSeg from .seg file format:
    ## the file to run in the example can be found in:
    ## https://software.broadinstitute.org/software/igv/SEG
    ## under example.seg file name.

    seg.file <- system.file("extdata", "DNACopy_output.seg", package = "CopyNumberPlots", mustWork = TRUE)
    cnv.call <- loadCopyNumberCallsSeg(seg.file = seg.file)

[Package CopyNumberPlots version 1.4.0 Index]