set_gene_rates: Assign pre-calculated regional mutation rates

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

Assign pre-calculated regional mutation rates

Description

This function allows you to specify regional rates of mutation–calculated however you like–to samples in your CESAnalysis. Rates can be assigned to all samples or to specified samples.

Usage

set_gene_rates(
  cesa = NULL,
  rates = NULL,
  samples = character(),
  missing_genes_take_nearest = FALSE
)

Arguments

cesa	CESAnalysis object
rates	A two-column data.table with either gene name or protein_id in column 1 and rate in column 2
samples	Which samples the input rates apply to. Defaults to all samples. Can be a vector of Unique_Patient_Identifiers, or a data.table containing rows from the CESAnalysis sample table.
missing_genes_take_nearest	Set to TRUE to have each gene/protein_id missing from rates take the rate of the nearest non-missing gene/protein.

Details

Provide rates in a data.table with two columns: gene name or protein ID (character) and rate (numeric, non-negative). Gene names or protein IDs must match those in CESAnalysis reference data. (Some reference data sets, such as ces.refset.hg19, only allow gene-level rates.) If you don't want to supply rates for every gene, set missing_genes_take_nearest = T to have each missing gene or coding region take the rate of the nearest non-missing one.

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.