process.xy.probes: Processes sex chromosome probes

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

Processes sex chromosome probes

Description

Identifies and processes sex chromosome probe information prior to CNA calling

Usage

process.xy.probes(normalized.data, sex.info)

Arguments

normalized.data	A gene by sample data-frame of normalized NanoString counts for all samples in experiment. First three column names must be 'CodeClass', 'Name', and 'Accession', followed by sample IDs. Sex chromosome probes are identified as those containing "chrX" and "chrY" labels in their 'Name' and/or 'Accession' values.
sex.info	A data-frame containing columns 'SampleID' and 'Sex' for each sample in 'normalized.data'. Recommended to use output of load.phenodata

Details

Sex chromosome probes are processed according to user-provided sample sex information. For female samples, chromosome Y probes are removed completely. For samples where sex information is not available, both chromosome X and Y probes are removed. For male samples, chromosome X and Y probe values are extracted and placed into a new data-frame, enabling separate downstream analysis.

Value

A list containing three items: 1) a data-frame holding 'normalized.data' with chrY probes removed from female samples, and chrX and chrY probes removed from both male samples and samples where sex is not available, 2) a data-frame holding 'normalized.data' for male chrX and chrY probes only (set to NULL if there are no male samples) and 3) names of all probes identified as belonging to sex chromosomes

Author(s)

Dorota Sendorek

Examples

	# load data
	data(NanoString.DNA.norm);
	data(PhenoData);

	# process chrX and chrY probes
	processed.data <- NanoStringNormCNV:::process.xy.probes(
		normalized.data = NanoString.DNA.norm,
		sex.info = PhenoData
		);

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