susie_finemap_region: Run fine-mapping for one region with SuSiE using summary...

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

Run fine-mapping for one region with SuSiE using summary statistics (susie_rss)

Description

Run fine-mapping with SuSiE using summary statistics for one LD block

Usage

susie_finemap_region(
  sumstats,
  R = NULL,
  snp_info = NULL,
  bigSNP = NULL,
  n = NULL,
  L = 1,
  prior_weights = NULL,
  estimate_residual_variance = FALSE,
  verbose = FALSE,
  save = FALSE,
  ...
)

Arguments

sumstats	A data frame of summary statistics
R	LD (correlation) matrix
snp_info	Variant information for the LD matrix.
bigSNP	a bigsnpr object attached via bigsnpr::snp_attach() containing the reference genotype panel.
n	GWAS sample size (optional, but strongly recommended.)
L	Number of causal signals.
prior_weights	A vector of prior probability for each SNP
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.

Value

a list of SuSiE results, and z-scores and LD (R) matrix used in SuSiE

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