Process fine-mapping summary statistics data

Process fine-mapping summary statistics data

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