gene_cs: Obtain credible gene sets from SNP-level gene mapping table

In kevinlkx/mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Obtain credible gene sets from SNP-level gene mapping table

Description

Obtain credible gene sets from SNP-level gene mapping table

Usage

gene_cs(gene.mapping.res, by.locus = TRUE, gene.cs.coverage = 0.8)

Arguments

gene.mapping.res	A data frame of SNP-level gene mapping table
by.locus	Logical, if TRUE, get credible gene sets based on locus-level gene PIP, If FALSE, get credible gene sets based on gene PIP.
gene.cs.coverage	A number between 0 and 1 specifying desired coverage of each credible gene set

Value

a data frame of credible gene set result. Columns: gene_cs: credible gene sets, gene_cs_locus_pip: credible gene sets and corresponding locus-level gene PIPs. gene_cs_pip: credible gene sets and corresponding gene PIPs. top_gene: genes with highest gene PIP at each locus. top_locus_gene_pip: locus-level gene PIP for the top gene. Locus-level gene PIP only includes SNPs within a locus, so this value may be lower than the gene PIP. top_gene_pip: gene PIP of the top gene.

kevinlkx/mapgen documentation built on March 31, 2024, 11:03 p.m.