effect_size: Direct effect sizes estimated from latent factor models

In lfmm: Latent Factor Mixed Models

Description

This function returns 'direct' effect sizes for the regression of X (of dimension 1) on the matrix Y, as usually computed in genome-wide association studies.

Usage

effect_size(Y, X, lfmm.object)

Arguments

Y	a response variable matrix with n rows and p columns. Each column is a response variable (numeric).
X	an explanatory variable with n rows and d = 1 column (numeric).
lfmm.object	an object of class lfmm returned by the lfmm_lasso or lfmm_ridge function.

Details

The response variable matrix Y and the explanatory variable are centered.

Value

a vector of length p containing all effect sizes for the regression of X on the matrix Y

Author(s)

Kevin Caye, Basile Jumentier, Olivier Francois

Examples

library(lfmm)

## Simulation of 1000 genotypes for 100 individuals (y)
u <- matrix(rnorm(300, sd = 1), nrow = 100, ncol = 3) 
v <- matrix(rnorm(3000, sd = 3), nrow = 3, ncol = 1000)
w <- u %*% v
y <- matrix(rbinom(100000, size = 2, 
                  prob = 1/(1 + exp(-0.3*(w
                  + rnorm(100000, sd = 2))))),
                  nrow = 100,
                  ncol = 1000)

#PCA of genotypes, 3 main axes of variation (K = 2) 
plot(prcomp(y))
  
## Simulation of 1000 phenotypes (x)
## Only the last 10 genotypes have significant effect sizes (b)
b <- matrix(c(rep(0, 990), rep(6000, 10)))
x <- y%*%b + rnorm(100, sd = 100)

## Compute effect sizes using lfmm_ridge
## Note that centering is important (scale = F).
mod.lfmm <- lfmm_ridge(Y = y, 
                  X = x,
                  K = 2)
              
## Compute direct effect sizes using lfmm_ridge estimates
b.estimates <- effect_size(y, x, mod.lfmm)

## plot the last 30 effect sizes (true values are 0 and 6000)
plot(b.estimates[971:1000])
abline(0, 0)
abline(6000, 0, col = 2)

## Prediction of phenotypes
candidates <- 991:1000 #set of causal loci 
x.pred <- scale(y[,candidates], scale = FALSE) %*% matrix(b.estimates[candidates])

## Check predictions
plot(x - mean(x), x.pred, 
     pch = 19, col = "grey", 
     xlab = "Observed phenotypes (centered)", 
     ylab = "Predicted from PRS")
     abline(0,1)
     abline(lm(x.pred ~ scale(x, scale = FALSE)), col = 2)

lfmm documentation built on June 30, 2021, 5:07 p.m.