fdr_thresh: FDR threshold and SNP highlighting

In etnite/bwardr: Brian Ward personal R package

FDR threshold and SNP highlighting

Description

FDR threshold and SNP highlighting

Usage

fdr_thresh(gwas_results, id, p, meth = "fdr", thresh = 0.05)

Arguments

gwas_results	A dataframe containing at least the following columns: 1) SNP identifiers 2) GWAS p-values. These should NOT be -log transformed
id	String specifying the name of the column in gwas_results containing SNP identifiers
p	Character specifying the name of the column in gwas_results containing GWAS output p-values
meth	String specifying the method of p-value adjustment to use - see output of help(p.adjust) for details
thresh	Number between 0 and 1 - the desired FDR threshold

Details

Adjusted p-values are calculated from a vector of p-values output from a GWAS analysis. If any adjusted p-values fall below the specified threshold, an approximate threshold for adjusted p-values is returned, with a list of the IDs of significant SNPs

Value

list consisting of

p.thresh	approximation of the FDR threshold for p-value distribution
sig.snps	vector of names of SNPs passing the FDR threshold

etnite/bwardr documentation built on Jan. 6, 2023, 7:12 a.m.