Extract significant results from .all files

This function scans the combine_1outcome folder for .all files, filters rows where Pass_FDR == "Pass" or Pass_Bonferroni == "Pass" (depending on pass_type argument), and writes the significant subset to a new file (e.g., smr_res_YYYYMMDD_iri3.sig.all).

Usage

leo_smr_extract_sig_res(dir, pass_type = c("FDR", "Bonferroni"), out_dir = "")

Arguments

dir

Character. The main combine_1outcome folder from combine_smr_res_1outcome.

pass_type

Character. Which significance criterion to use: one of c("FDR", "Bonferroni", "both"). - "FDR": keep rows where Pass_FDR == "Pass" - "Bonferroni": keep rows where Pass_Bonferroni == "Pass" - "both": keep rows where either FDR or Bonferroni is "Pass"

out_dir

Character. Where to write significant results. Default dir/combine_1outcome/sig.

Value

NULL. Writes .sig.all files to disk.

Examples

if (FALSE) { # \dontrun{
# For the directory "/Users/leoarrow/project/iridocyclitis/output/smr-t2d",
# after running combine_smr_res_1outcome, we have .all files in
# "smr-t2d/combine_1outcome".

leo_smr_extract_sig_res(
  dir       = "/Users/leoarrow/project/iridocyclitis/output/smr-t2d",
  pass_type = "FDR"
)
} # }