test_gene_list_in_exposures {YAPSA} | R Documentation

## Test if mutated PIDs are enriched in signatures

### 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

     NULL

[Package YAPSA version 1.16.0 Index]