Runs cTWAS post-processing procedure for merging regions

Usage

postprocess_LD_mismatch(
  region_data,
  z_snp,
  weights,
  LD_map,
  snp_map,
  gwas_n,
  finemap_res,
  susie_alpha_res,
  group_prior = NULL,
  group_prior_var = NULL,
  min_nonSNP_PIP = 0.8,
  filter_cs = FALSE,
  p_diff_thresh = 5e-06,
  pip_thresh = 0.5,
  z_thresh = NULL,
  plot = TRUE,
  maxSNP = Inf,
  ncore = 1,
  verbose = FALSE,
  logfile = NULL,
  ...
)

Arguments

region_data: region_data to be fine-mapped.
z_snp: A data frame with columns: "id", "z", giving the z-scores for SNPs.
weights: a list of preprocessed weights.
LD_map: a data frame with filenames of LD matrices for the regions.
snp_map: a list of data frames with SNP-to-region map for the reference.
gwas_n: integer, GWAS sample size.
finemap_res: a data frame of original finemapping result.
susie_alpha_res: a data frame of original susie alpha result.
group_prior: a vector of prior inclusion probabilities for different groups. If NULL, it will use uniform prior inclusion probabilities.
group_prior_var: a vector of prior variances for different groups. If NULL, it will set prior variance = 50 as the default in susie_rss.
min_nonSNP_PIP: regions with total non-SNP PIP >= min_nonSNP_PIP will be selected to run LD mismatch diagnosis.
filter_cs: If TRUE, computes region non-SNP PIP only in credible sets.
p_diff_thresh: p-value cutoff for identifying problematic SNPs with significant difference between observed z-scores and estimated values.
pip_thresh: cutoff of gene PIP to select problematic genes.
z_thresh: cutoff of abs(z-scores) to select problematic genes.
plot: If TRUE, plot observed z-score vs the expected value.
maxSNP: Inf or integer. Maximum number of SNPs in a region. Default is Inf, no limit. This can be useful if there are many SNPs in a region and you don't have enough memory to run the program.
ncore: The number of cores used to parallelize computation over regions
verbose: If TRUE, print detail messages.
logfile: the log file, if NULL will print log info on screen
...: Additional arguments of finemap_regions.

Value

a list with region merge results.