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

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

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