test_gene_list_in_exposures: Test if mutated PIDs are enriched in signatures

In eilslabs/YAPSA: Yet Another Package for Signature Analysis

Description

For all signatures found in a project, this function tests whether PIDs having mutations in a specified list of genes of interest have significantly higher exposures.

Usage

test_gene_list_in_exposures(in_gene_list, in_exposure_df, in_mut_table,
  in_gene.field = "GENE_short", in_p_cutoff = 0.05)

Arguments

in_gene_list	List with genes of interest
in_exposure_df	Data frame with the signature exposures
in_mut_table	Data frame or table of mutations (derived from vcf-format)
in_gene.field	Name of the column in which the gene names are to be looked up
in_p_cutoff	Significance threshold

Value

A list with entries pvals, exposure_df, number_of_mutated,

• pvals: p-values of the t-tests performed on mutated vs. unmutated PIDs

• exposure_df: Transposed input exposures data frame with additional annotations for mutation status

• number_of_mutated: Number of PIDs carrying a mutation

Examples

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eilslabs/YAPSA documentation built on May 16, 2019, 1:23 a.m.