testColoc: Wrapper around coloc.abf to directly work with tidy data...

In kauralasoo/seqUtils:

Description

Group QTL database by gene, sort by p_nominal, keep SNP with smallest p-value, correct that using bonferroni correction and then apply FDR correction across genes.

Usage

testColoc(df1, df2, n1, n2, p1 = 1e-04, p2 = 1e-04, p12 = 1e-05)

Arguments

df1	Summary statistics from the first dataset (required columns: snp_id, p_nominal, beta, MAF).
n1	Sample size of the first dataset.
n2	Sample size of the second dataset.
p1	prior probability a SNP is associated with trait 1, default 1e-4
p2	prior probability a SNP is associated with trait 2, default 1e-4
p12	prior probability a SNP is associated with both traits, default 1e-5
df1	Summary statistics from the second dataset (required columns: snp_id, p_nominal, beta, MAF).

Value

List of colocalisation results (Same as coloc.abf).

kauralasoo/seqUtils documentation built on May 20, 2019, 7:42 a.m.