compute_gene_pip: Compute gene PIPs based on fine-mapping result and functional...

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

Compute gene PIPs based on fine-mapping result and functional annotations.

Description

Compute gene PIPs based on fine-mapping result and functional annotations.

Usage

compute_gene_pip(
  finemapstats,
  genomic.annots,
  intron.mode = FALSE,
  d0 = 50000,
  exon.weight = 1,
  loop.weight = 1,
  cols.to.keep = c(names(mcols(finemapstats)), "gene_name", "category", "weight",
    "frac_pip", "gene_pip")
)

Arguments

finemapstats	A GRanges object of fine-mapping result.
genomic.annots	A list of GRanges objects of genomic annotations.
intron.mode	Logical. If TRUE, assign intronic SNPs to genes containing the introns.
d0	A scaling parameter used for computing weight based on SNP-gene distance. Weight = exp(-dist/d0). Default = 50000 (50kb).
exon.weight	Weight for exon (and promoter) categories (default = 1).
loop.weight	Weight for chromatin loop categories (default = 1).
cols.to.keep	columns to keep in the SNP gene weights

Value

A data frame of gene mapping result

kevinlkx/Mapgen documentation built on April 2, 2024, 5:48 a.m.