loadCopyNumberCallsPanelcnmops {CopyNumberPlots} | R Documentation

## loadCopyNumberCallsPanelcnmops

### Description

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

### Usage

    loadCopyNumberCallsPanelcnmops(panelcn.mops.res, chr.col = NULL, start.col = NULL, end.col = NULL, cn.col = NULL, segment.value.col = NULL, genome = NULL, verbose = TRUE)

### Arguments

`panelcn.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 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` | (character) Whether to show information messages. (defaults to TRUE)

### Details

This function will load segments data from panelcn.mops resulttable or in a tabular format or 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. 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

    ## loadCopyNumberCallsPanelcnmops from panelcn.mops resulttable:
    library(panelcn.mops)
    data(panelcn.mops, package = "panelcn.mops")
    XandCB <- test
    sampleNames <- colnames(elementMetadata(XandCB))
    elementMetadata(XandCB) <- cbind(elementMetadata(XandCB), elementMetadata(control))

    resulttable <- createResultTable(resultlist = resultlist, XandCB = XandCB, countWindows = countWindows, sampleNames = sampleNames)
    panelcn.mops.res <- resulttable[[1]]
    cnv.call <- loadCopyNumberCallsPanelcnmops(panelcn.mops.res = panelcn.mops.res)

[Package CopyNumberPlots version 1.0.1 Index]