gene_level_changes: Get gene-level changes in copy number from FACETS output.

In mskcc/facets-suite: Functions to run and parse output from FACETS

Get gene-level changes in copy number from FACETS output.

Description

This maps protein-coding genes onto copy-number segmentation from FACETS output derives the copy-number status from that, based on the integer copy number. Additionally, the copy-number log-ratio of the SNPs falling insided the gene boundaries are used to perform a Z-test against the dipLogR baseline.

Usage

gene_level_changes(facets_output, genome = c("hg19", "hg38"),
  algorithm = c("em", "cncf"))

Arguments

facets_output	Full FACETS output from run_facets.
genome	Genome build.
algorithm	Choice between FACETS em and cncf algorithm.

Value

data.frame for all genes mapping onto a segment in the output segmentation, with the columns:

• median_cnlr_seg: Median copy-number log-ratio for segment.

• genes_on_seg: Protein-coding genes on segment.

• gene_snps: Median copy-number log-ratio for segment.

• gene_het_snps: Median copy-number log-ratio for segment.

• spans_segs: Boolean indicating whether the gene boundaries map onto different segments.

• cn_state: Label for coyp-number configuration.

• tsg: Boolean indicating whether gene is a tumor suppressor.

Examples

## Not run: 
gene_level_changes(test_facets_output, 'hg38', 'em')

## End(Not run)

mskcc/facets-suite documentation built on Sept. 13, 2022, 4:14 a.m.