Gets problematic genes from problematic SNPs

Source: R/ctwas_diagnose_LD_mismatch.R

Gets problematic genes from problematic SNPs

get_problematic_genes(
  problematic_snps,
  weights,
  finemap_res,
  pip_thresh = 0.5,
  z_thresh = 3
)

Arguments

problematic_snps

a character vector of problematic SNP rsIDs

weights

a list of weights

finemap_res

a data frame of cTWAS finemapping results

pip_thresh

cutoff of gene PIP to select genes

z_thresh

cutoff of abs(z-scores) to select genes

Value

a vector of problematic genes