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

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

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