run_finemapping: Run functional fine-mapping using summary statistics

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

Run functional fine-mapping using summary statistics

Description

Run fine-mapping with SuSiE using summary statistics for all LD blocks with prior probabilities

Usage

run_finemapping(
  sumstats,
  bigSNP = NULL,
  region_info = NULL,
  n = NULL,
  priortype = c("torus", "uniform", "custom"),
  prior_weights = NULL,
  L = 1,
  estimate_residual_variance = FALSE,
  verbose = FALSE,
  save = FALSE,
  outputdir = getwd(),
  outname = NULL,
  ...
)

Arguments

sumstats	A data frame of summary statistics
bigSNP	a bigsnpr object attached via bigsnpr::snp_attach() containing the reference genotype panel.
region_info	A data frame of region information, paths of LD matrices (R, correlation matrices), and paths of variant information files corresponding to the LD matrices.
n	The sample size (optional, but strongly recommended.)
priortype	prior type: 'torus' (use the 'torus_prior' in sumstats), 'uniform' (uniform prior), or 'custom' (use the values provided in prior_weights).
prior_weights	A vector of prior probability for each SNP.
L	Number of causal signals. If L = 1, bigSNP or region_info are not required.
estimate_residual_variance	The default is FALSE, the residual variance is fixed to 1 or variance of y. If the in-sample LD matrix is provided, we recommend setting estimate_residual_variance = TRUE.
verbose	If TRUE, print progress.
save	If TRUE, save SuSiE result and LD (R) matrix for each locus.
outputdir	Directory of SuSiE result
outname	Filename of SuSiE result

Value

A list of SuSiE results; one per LD block.

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