CCGWAS: CC-GWAS

In wouterpeyrot/CCGWAS:

CC-GWAS

Description

Function to run CC-GWAS to test for differences in allele frequency among cases of two different disorders using summary statistics from the respective case-control GWAS. See Peyrot and Price. 2020 bioRxiv for details. A more detailed description is available here: https://github.com/wouterpeyrot/CCGWAS.

Usage

CCGWAS( outcome_file , A_name , B_name , sumstats_fileA1A0 , sumstats_fileB1B0 , K_A1A0 , K_A1A0_high , K_A1A0_low , K_B1B0 , K_B1B0_high , K_B1B0_low ,
        h2l_A1A0 , h2l_B1B0 , rg_A1A0_B1B0 , intercept_A1A0_B1B0 , m , N_A1 , N_B1 , N_A0 , N_B0 , N_overlap_A0B0 , ...)

Arguments

outcome_file	The name of the file where the outcome should be saved.
A_name/B_name	2 or 3 letter disorder codes that will be used to plot the genetic distance between cases and controls in terms of FST,causal.
sumstats_fileA1A0/sumstats_fileB1B0	Names of the gzip-files with case-control GWAS results. Column names should be: SNP, CHR, BP, EA, NEA, FRQ, OR, SE, P, Neff.
K_A1A0/K_B1B0	The most likely lifetime disorder prevalences of disorder A and disorder B in the population, following the disorder definition used in the respective case-control GWAS.
K_A1A0_high/K_B1B0_high	Upper bound of disorder prevalences.
K_A1A0_low/K_B1B0_low	Lower bound of disorder prevalences.
h2l_A1A0/h2l_B1B0	SNP-based heritability on the liability scale.
rg_A1A0_B1B0	Genetic correlation between disorders A and B.
intercept_A1A0_B1B0	Intercept from cross-trait LD score regression.
m	Approximation of number of independent effective loci.
N_A1/N_B1	Total number of cases in the respective input case-control GWAS.
N_A0/N_B0	Total number of controls in the respective input case-control GWAS.
N_overlap_A0B0	Confirmed number of overlapping controls between the A1A0 and B1B0 GWAS samples.
subtype_data	Set to FALSE when comparing two different disorders (with different definitions of controls, e.g. when comparing psychiatric disorders). Set to TRUE when comparing subtypes of a disorder (with same definition of controls, e.g. when comparing subtypes of specific cancer).
sumstats_fileA1B1	Set to NA when applying CC-GWAS based on case-control GWAS results only. Specify the name of the gzip-file with GWAS results from the direct case-case comparison, when applying CC-GWAS+.
N_A1_inA1B1/N_B1_inA1B1	Set to NA when applying CC-GWAS based on case-control GWAS results only. When applying CC-GWAS+, specify the number of cases in the direct case-case GWAS here.
intercept_A1A0_A1B1/intercept_B1B0_A1B1	Set to NA when applying CC-GWAS based on case-control GWAS results only. When applying CC-GWAS+, provide here the intercept from cross-trait LD score regression of A1A0 vs A1B1 respectively B1B0 vs A1B1.

Value

The output consists of three output files. The 'outcome_file.log' file provides a logfile of the analyses. This file also reports the CC-GWAS_OLS weights and the CC-GWAS_Exact weights. The 'outcome_file.pdf' file provides a plot of the genetic distances between cases and controls of both disorders in terms of F_ST,causal. The 'outcome_file.results.gz' file reports results of the case-case association analyses. SNPs with significant case-case association are labelled as 1 in the 'CCGWAS_signif' column. See for more details: https://github.com/wouterpeyrot/CCGWAS.

Don't forget to prepare your results for follow-up analyses! See: https://github.com/wouterpeyrot/CCGWAS#preparing-cc-gwas-results-for-follow-up-analyses.

wouterpeyrot/CCGWAS documentation built on Sept. 1, 2022, 11:43 p.m.