calculate.replicate.concordance: Determine copy number concordance across replicate samples

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

Determine copy number concordance across replicate samples

Description

Quantifies CNA call concordance for all genes/probes found across sample replicates

Usage

calculate.replicate.concordance(cna.rounded.reps, phenodata.reps)

Arguments

cna.rounded.reps	A gene by sample data-frame of CNA calls for all replicate samples. Column names must match sample IDs found in 'phenodata.reps'.
phenodata.reps	A data-frame containing sample annotation for all replicate samples. Must include columns 'Name' and 'SampleID'. Replicates belonging to a single sample are identified as such by their matching sample names (phenodata column 'Name'). See output of load.phenodata

Value

A gene by sample name data-frame of concordance values (1 signifies matching CN values, 0 signifies discordant CN values)

Author(s)

Cindy Yao and Emilie Lalonde

See Also

NanoStringNormCNV:::calculate.replicate.variance

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