loadCopyNumberCallspennCNV {CopyNumberPlots} | R Documentation

## loadCopyNumberCallspennCNV

### Description

Loads copy number calls from pennCNV.rawcnv file format

### Usage

    loadCopyNumberCallspennCNV (pennCNV.file, chr.col = NULL, start.col = NULL, end.col = NULL, cn.col = NULL, segment.value.col = NULL, genome = NULL, verbose=TRUE)

### Arguments

`pennCNV.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 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 NULL)
`segment.value.col` | (number or character) The name or number of the column with segment value. If NULL, it is automatically identified. (defaults to NULL)
`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 copy number calls from pennCNV.rawcnv 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 or a list of GRanges with a GRanges per sample.

### Examples

    ## loadCopyNumberCallspennCNV from .rawcnv file format:
    ## The file to run the example can be found in: http://penncnv.openbioinformatics.org/en/latest/user-guide/test/

    pennCNV.file <- system.file("extdata", "pennCNV.rawcnv", package = "CopyNumberPlots", mustWork = TRUE)
    cnv.call <- loadCopyNumberCallspennCNV(pennCNV.file = pennCNV.file)

[Package CopyNumberPlots version 1.0.1 Index]