test_by_wFDX: Perform hypothesis testing using weighted false discovery...

In hillarykoch/locdiffr: analysis of LOCal DIFFerences in chromatin aRchitecture

Description

Perform hypothesis testing using weighted false discovery controlling quantities wFDR and/or wFDX.

Usage

test_by_wFDR(scc_scan_file, sampled_nngps_file, outpath, alpha = .01, nthresh = 100, return = FALSE)
test_by_wFDX(scc_scan_file, sampled_nngps_file, outpath, alpha = .01, beta = 0.01, nthresh = 100, return = FALSE)

Arguments

scc_scan_file	Path to the rds file output by run_scc_scan
sampled_nngps_file	Path to the rds file output by sample_new_nngps
outpath	Path to where the output will be written. The output file should be given the .rds file extension.
alpha	Confidence level at which to control false discoveries for the hypothesis text.
beta	Additional exceedance threshold used for testing wFDX. Recommended to set to the same value as alpha.
nthresh	Number of thresholds used to approximate wFDR and wFDX. Defaults to 100.
return	Logical. Should the output also be returned by the function?

Value

If return = TRUE, this function outputs a list of genomic loci and an indicator of whether or not the locus was rejected.

Examples

# Compute rejections based on weighted false discovery rate
test_by_wFDR(
    scc_scan_file = "inst/extdata/output/z.rds",
    sampled_nngps_file = "inst/extdata/output/pred.rds",
    outpath = "inst/extdata/output/wfdr.rds",
    alpha = 0.1
    )

# Compute rejections based on weighted false discovery exceedence
test_by_wFDX(
    scc_scan_file = "inst/extdata/output/z.rds",
    sampled_nngps_file = "inst/extdata/output/pred.rds",
    outpath = "inst/extdata/output/wfdx.rds",
    alpha = 0.1,
    beta = 0.1
    )

hillarykoch/locdiffr documentation built on April 25, 2021, 6:26 p.m.