get.cna.thresholds: Determine thresholds for CNA calling

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

Determine thresholds for CNA calling

Description

Determine tumour:normal count ratio thresholds used for calling CNA states. Basic formula is median - x*SD.

Usage

get.cna.thresholds(ratios, percent = 0.8)

Arguments

ratios	A vector of tumour:normal ratios. See output of NanoStringNormCNV:::get.tumour.normal.ratio
percent	The percent of density you would like to have between the threshold bounds (0.1 - 0.99). Default is 0.8

Details

Returns the ratio thresholds that should be used to call CNA states for a given set of tumour:normal ratios. Thresholds are based on the standard deviations of the central 50% of probes. Kernel type is gaussian.

Value

A data-frame of 2 thresholds

Author(s)

Emilie Lalonde and Veronica Sabelnykova

Examples

NanoStringNormCNV:::get.cna.thresholds(ratios = rnorm(1000, 5, 4), percent = 0.9);

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