process_finemapping_sumstats: Process fine-mapping summary statistics data

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

Process fine-mapping summary statistics data

Description

Process fine-mapping summary statistics data

Usage

process_finemapping_sumstats(
  finemapstats,
  snp = "snp",
  chr = "chr",
  pos = "pos",
  pip = "pip",
  pval = "pval",
  zscore = "zscore",
  cs = "cs",
  locus = "locus",
  pip.thresh = 0,
  filterCS = FALSE,
  maxL = 10
)

Arguments

finemapstats	A data frame of fine-mapping summary statistics
snp	Name of the SNP ID (rsID) column in the fine-mapping summary statistics
chr	Name of the chr column in the fine-mapping summary statistics
pos	Name of the position column in the fine-mapping summary statistics
pip	Name of the PIP column in the fine-mapping summary statistics
pval	Name of the P-value column in the fine-mapping summary statistics
zscore	Name of the z-score column in the fine-mapping summary statistics
cs	Name of the credible set (CS) column in the fine-mapping summary statistics
locus	Name of the locus column in the fine-mapping summary statistics
pip.thresh	Select SNPs by PIP threshold (default = 0, no filtering).
filterCS	If TRUE, limiting to SNPs within credible sets.
maxL	Maximum number of credible sets (default = 10). If filterCS is TRUE, it will only keep SNPs with credible set (CS) number >= 1 and <= maxL.

Value

A GRanges object with cleaned and filtered fine-mapping summary statistics

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