tumour.normal.ratio.to.cn.state: Convert tumour:normal count ratios into discrete copy number...

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

Convert tumour:normal count ratios into discrete copy number (CN) states

Description

Convert tumour:normal count ratios into copy number states for a set of probes

Usage

tumour.normal.ratio.to.cn.state(ratios, thresholds)

Arguments

ratios	A vector of tumour:normal count ratios. See output of NanoStringNormCNV:::get.tumour.normal.ratio
thresholds	A 4-item vector specifying homozygous loss, heterozygous loss, single-copy gain and multi-copy gain, respectively. Order is important! See output of NanoStringNormCNV:::get.cna.thresholds

Details

Copy number states differ from actual copy number values by representing the copy number deviation (i.e. -2, -1, 0, 1, 2+) from an expected neutral copy number (i.e. 2) and not the copy number itself (i.e. 0, 1, 2, 3, 4+).

Value

A vector of copy number states

Author(s)

Emilie Lalonde

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