loadCopyNumberCalls {CopyNumberPlots} | R Documentation

## loadCopyNumberCalls

### Description

Loads copy number calls from a tabular format

### Usage

    loadCopyNumberCalls(cnv.data, chr.col = NULL, start.col = NULL, end.col = NULL, cn.col = NULL, loh.col = NULL, segment.value.col = NULL, genome = NULL, verbose = TRUE)

### Arguments

`cnv.data` | Either the name of the file with the data or a variable containing 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)
`loh.col` | (number or character) The name or number of the column with LOH 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 segments data from any "bed-like" data structure in R 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

### Examples

    df <- data.frame("id"= "rs1234","chromosome"="chr1", "Start"=0, "end.position"=100,
    "copy.number.level"=3, "LOH"=0, "median.value.per.segment"=1.2,
    "BAF"=0.2, "Log Ratio"=1.5, "strange.name"="strange.value")

    cnv.call <- loadCopyNumberCalls(cnv.data = df)

[Package CopyNumberPlots version 1.4.0 Index]