iGWAS example - Coronary Artery Disease

Preparing data

As input, the function requires the p-values and sample sizes of the two GWAS studies.

First, we load in the example data which consists of p-values for all 514,178 SNPs tested in both the C4D and CARDIoGRAM association analyses, as well as the number of cases and controls in each study. The input P value vectors should be of the same size, and in the same order.

The example data file is ~5MB in size and can be downloaded directly from github into R:

#uncomment on Windows
#setInternet2(use = TRUE)
download.file("http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData", destfile = "exampledata", method = "libcurl")
load("exampledata")

We calculate the effective sample size of each study as:

c4d_ss <- 4/(1/c4d_ncases + 1/c4d_ncontrols)
cardiogram_ss <- 4/(1/cardiogram_ncases + 1/cardiogram_ncontrols)

We are now ready to run iGWAS.

iGWAS analysis: the basics

The simplest way to run iGWAS is using default settings. The default setting uses Bayes weights. Each of the weighting functions, and the iGWAS routine, make assumptions about the input data; these are explored more fully in the “Pweight Basics” vignette.

As an example, we use the larger CARDIoGRAM study (# cases = 22233, # controls = 64762) to weight the C4D data (# cases = 15420, # controls = 15062):

source("../R/iGWAS.R")
source("../R/bayes_weights.R")
res_default <- iGWAS(P_current=cad$P_c4d, N_current=c4d_ss, P_prior=cad$P_cardiogram, N_prior=cardiogram_ss)

## Number of significant tests using bayes weights and genome-wide correction: 41

40 SNPs are genome-wide significant (P < 5e-8) after weighting. We can check whether weighting increases the number of genome-wide hits, versus using the original data with no prior knowledge:

cat(c("Number of genome-wide significant SNPs (P < 5e-8) with no weighting: ", sum(cad$P_c4d < 5e-8) ))

## Number of genome-wide significant SNPs (P < 5e-8) with no weighting:  29

In this example, p-value weighting increases the number of genome-wide significant SNPs from 29 to 40. Further analyses would be needed to determine whether the 11 additional SNPs are in linkage disequilibrium with the 29, or whether they represent new and independent loci.

We can inspect the correspondence between weights and p-values from the prior-knowledge CARDIoGRAM study:

w = res_default$w
plot(-log10(cad$P_cardiogram), w, main="How Bayes weights depend on p-values", ylab=expression(italic(w)), xlab=expression(-log[10](italic(p))))

cat(c("Maximum weight reached at P-value of ", cad$P_cardiogram[which.max(w)] ))

## Maximum weight reached at P-value of  1.12e-09

Weight increases with decreasing P value until it reaches a maximum, then decreases. Lower weight is assigned to SNPs with P values below 1.12e-09, as these SNPs are expected to have a very low P values in the current C4D study, and not require weighting to attain significance.

Visualizing iGWAS results

For the common task of visualizing of significant P values, before and after weighting, there is a built-in option figure="T" in the iGWAS function. This also requires us to pass in the GWAS data frame with the parameter GWAS_data_frame=cad.

The iGWAS function calls the qqman package to generate the Manhattan plot (qqman must be installed). This package is described in: Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).

Note: Drawing the manhattan plot may take a few minutes, depending on the number of SNPs being plotted.

res_default <- iGWAS(P_current=cad$P_c4d, N_current=c4d_ss, P_prior=cad$P_cardiogram, N_prior=cardiogram_ss,figure="T", GWAS_data_frame=cad)

## Number of significant tests using bayes weights and genome-wide correction: 41

Here, unweighted P values are shown in black and weighted P values in green. The red line corresponds to the threshold for genome-wide significance.

From this plot, it is visually apparent that weighting has boosted new loci to genome-wide significance, e.g. on chromosome 9.

The impact of other parameters

The dispersion factor phi affects the degree of regularization for Bayes weights. Setting phi = 0 corresponds to using Spjotvoll weights. Here, we test how different values of phi affect the number of significant loci discovered.

source("../R/spjotvoll_weights.R")
phi=seq(0,1,by=0.1)
numSNP <- sapply(phi,function(x){sum(iGWAS(P_current=cad$P_c4d, N_current=c4d_ss, P_prior=cad$P_cardiogram, N_prior=cardiogram_ss, phi=x)$sig_ind)})

## Number of significant tests using bayes weights and genome-wide correction: 44 
## Number of significant tests using bayes weights and genome-wide correction: 44 
## Number of significant tests using bayes weights and genome-wide correction: 44 
## Number of significant tests using bayes weights and genome-wide correction: 45 
## Number of significant tests using bayes weights and genome-wide correction: 44 
## Number of significant tests using bayes weights and genome-wide correction: 44 
## Number of significant tests using bayes weights and genome-wide correction: 44 
## Number of significant tests using bayes weights and genome-wide correction: 44 
## Number of significant tests using bayes weights and genome-wide correction: 42 
## Number of significant tests using bayes weights and genome-wide correction: 42 
## Number of significant tests using bayes weights and genome-wide correction: 41

plot(phi, numSNP, type="o", main="Choice of phi impacts the number of significant SNPs", ylab="# SNPs", xlab=expression(phi))

cat(c("Choice of phi that maximizes the number of genome-wide significant SNPs:", phi[which.max(numSNP)] ))

## Choice of phi that maximizes the number of genome-wide significant SNPs: 0.3