getdels: Extract putative CNVs from a set of segments
In malemay/delgbs: Detection of deletions and duplications from GBS data

getdels

R Documentation

Extract putative CNVs from a set of segments

Description

This function identifies a set of segments representing putative CNVs ( homozygous deletions, hemizygous deletions or duplications) from a set of segments and associated mean log2 ratio values, and outputs them as a data.frame along with some metadata describing them.

Usage

getdels(data, ind, all_segments = FALSE, homdel = -2, hetdel = -0.2,
  dup = 0.2)

Arguments

`data`	a data.frame representing a set of segments.
`ind`	a character vector of length one. The sample (individual) for which to extract the putative CNVs.
`all_segments`	logical of length one (`TRUE` or `FALSE`). Should all segments be extracted and output? Defaults to `FALSE`, meaning that only segments representing putative CNVs are output.
`homdel`	a single numeric value. The threshold to be used for calling homozygous deletions; all segments with a mean log2 ratio less than this values is considered called as a homozygous deletion.
`hetdel`	a single numeric value. The threshold to be used for calling hemizygous deletions; all segments with a mean log2 ratio less than this value and great than or equal to `homdel` is called as a hemizygous deletion.
`dup`	a single numeric value. The threshold to be used for calling duplications; all segments with a mean log2 ratio larger than this value is called as a duplication.