get.tumour.normal.ratio: Calculate tumour:normal ratios

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

Calculate tumour:normal ratios

Description

Calculates tumour:normal ratios using NanoString count data

Usage

get.tumour.normal.ratio(normalized.data, reference, chip.info = NULL, per.chip = FALSE)

Arguments

normalized.data	A gene by sample data-frame of normalized NanoString counts of tumour and reference samples. First three column names must be 'CodeClass', 'Name', and 'Accession', followed by sample IDs.
reference	A vector of the reference sample name(s)
chip.info	A data-frame of chip information for each sample in 'normalized.data', including columns 'Cartridge' and 'SampleID', or NULL (default). Required if 'per.chip' = TRUE. Recommended to use output of load.phenodata
per.chip	Whether to use only the reference sample(s) specific to a given chip. Defaults to FALSE.

Value

A gene by sample data-frame of tumour:normal ratios

Author(s)

Emilie Lalonde

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