apply.kd.cna.thresh: Determine the copy number (CN) values from ratios using a...

In uclahs-cds/public-R-NanoStringNormCNV: Helper Functions to Normalize NanoString CNV Data

Determine the copy number (CN) values from ratios using a kernel density approach

Description

Determine the copy number values from count ratios by first calculating thresholds using a kernel density approach

Usage

apply.kd.cna.thresh(ratio.data, kd.values, neutral.cn = 2)

Arguments

ratio.data	A gene by sample data-frame of tumour:normal ratios. See output of NanoStringNormCNV::get.tumour.normal.ratio
kd.values	A 2- or 4-element vector containing the kernel density values to be used to calculate copy number thresholds. Order is important. For 4 elements, values define homozygous deletion, heterozygous deletion, single copy gain, and multi-copy gain. For 2 elements, values define heterozygous deletion/gain and homozygous deletion/gain.
neutral.cn	The expected neutral copy number; i.e. 2 for autosomes/female chrX (default), 1 for male sex chromosomes. This value is used to calculate the observed copy number values by summing it with generated copy number states: -2, -1, 0, 1, 2 (see output of NanoStringNormCNV:::tumour.normal.ratio.to.cn.state).

Details

Determine the copy number values (0, 1, 2, 3, 4) of each probe from raw tumour:normal count ratios using thresholds derived from requested kernel densities ('kd.values').

Value

A gene by sample data-frame of copy number values

Author(s)

Cindy Yao and Emilie Lalonde

See Also

NanoStringNormCNV:::apply.ns.cna.thresh

uclahs-cds/public-R-NanoStringNormCNV documentation built on May 31, 2024, 9:09 p.m.