Diagnose LD mismatch using SuSiE RSS

Diagnose LD mismatch using SuSiE RSS

diagnose_LD_mismatch_susie(
  z_snp,
  region_ids,
  LD_map,
  gwas_n,
  p_diff_thresh = 5e-08,
  LD_format = c("rds", "rdata", "mtx", "csv", "txt", "custom"),
  LD_loader_fun,
  ncore = 1,
  logfile = NULL
)

Arguments

z_snp

A data frame with two columns: "id", "A1", "A2", "z". giving the z scores for snps. "A1" is effect allele. "A2" is the other allele.

region_ids

A vector of region IDs to run diagnosis

LD_map

a data frame with filenames of LD matrices and SNP information for each of the regions.

gwas_n

integer, GWAS sample size.

p_diff_thresh

numeric, p-value threshold for identifying problematic SNPs with significant difference between observed z-scores and estimated values

LD_format

file format for LD matrix. If "custom", use a user defined LD_loader_fun() function to load LD matrix.

LD_loader_fun

a user defined function to load LD matrix when LD_format = "custom".

ncore

integer, number of cores for parallel computing.

logfile

the log file, if NULL will print log info on screen

Value

a list of problematic SNPs, flipped SNPs, and test statistics from susie's `kriging_rss` function