collapse.genes: Collapse probe counts per gene

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

Collapse probe counts per gene

Description

Collapse counts of all probes belonging to the same gene

Usage

	collapse.genes(normalized.data)

Arguments

normalized.data

A gene by sample data-frame of normalized NanoString counts. First three column names must be 'CodeClass', 'Name', and 'Accession', followed by sample IDs. Probes to be collapsed together are identified by their matching 'Accession' values.

Details

Collapse counts for probes belonging to the same gene (only performed on 'Endogenous' or 'Housekeeping' probes). Collapsing is done by taking the mean count.

Value

A gene by sample data-frame of collapsed counts, where first three column names are 'CodeClass', 'Name', and 'Accession'.

Author(s)

Cindy Yao

Examples

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

	# collapse probes by gene
	NanoString.DNA.norm <- collapse.genes(normalized.data = NanoString.DNA.norm);

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