callAlterationsFromSegmentation {PureCN} | R Documentation

## Calling of amplifications and deletions from segmentations

### Description

This function can be used to obtain gene-level copy number calls from segmentations. This is useful for comparing PureCN's segmentations with segmentations obtained by different tools on the gene-level. Segmentation file can contain multiple samples.

### Usage

    callAlterationsFromSegmentation(sampleid, chr, start, end, num.mark = NA,
      seg.mean, C, gc.gene.file, fun.focal = findFocal, args.focal = list(),
      ...)

### Arguments

`sampleid` | The sampleid column in the segmentation file.
`chr` | The chromosome column.
`start` | The start positions of the segments.
`end` | The end positions of the segments.
`num.mark` | Optionally, the number of probes or markers in each segment.
`seg.mean` | The segment mean.
`C` | The segment integer copy number.
`gc.gene.file` | A mapping file that assigns GC content and gene symbols to each exon in the coverage files. Used for generating gene-level calls. First column in format CHR:START-END. Second column GC content (0 to 1). Third column gene symbol. This file can be generated with the ‘GATK GCContentByInterval’ tool or with the `calculateGCContentByInterval` function.
`fun.focal` | Function for identifying focal amplifications. Defaults to `findFocal`.
`args.focal` | Arguments for focal amplification function.
`...` | Arguments passed to `callAlterations`.

### Value

A list of `callAlterations` `data.frame` objects, one for each sample.

### Author(s)

Markus Riester

### Examples

    data(purecn.example.output)
    seg <- purecn.example.output$results[[1]]$seg
    gc.gene.file <- system.file("extdata", "example_gc.gene.file.txt",
            package = "PureCN")

    calls <- callAlterationsFromSegmentation(sampleid=seg$ID, chr=seg$chrom,
        start=seg$loc.start, end=seg$loc.end, num.mark=seg$num.mark,
        seg.mean=seg$seg.mean, C=seg$C, gc.gene.file=gc.gene.file)

[Package PureCN version 1.8.1 Index]