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Add FDR (q-values) to per-window top hits across chromosomes

Source: R/step_add_fdr.R
cacti_add_fdr.Rd

Reads per-chromosome CACTI window result files, computes per-window top-hit summaries (min p, Bonferroni, ACAT across SNPs in the window), and assigns q-values to the ACAT top-hit p-values.

Usage

cacti_add_fdr(file_all_pval, file_fdr_out)

Arguments

file_all_pval

a character vector containing all pvalue file paths. e.g., "c(chr1.txt.gz, chr2.txt.gz, chr3.txt.gz)"

file_fdr_out

Output filename for combined results with FDR.

Value

Invisibly returns the combined results with FDR.; writes file_fdr_out.

Details

Expected columns in each file:

  • group : window / peak-group ID

  • snp : variant ID

  • pval : p-value per (snp, group)