fdr_thresh: FDR threshold and SNP highlighting

Description Usage Arguments Details Value

View source: R/fdr_thresh.R

Description

FDR threshold and SNP highlighting

Usage

1
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 April 14, 2021, 7:04 p.m.