bed.loadings: SNP loadings

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

SNP loadings

Description

Compute the loadings corresponding to given PCs.

Usage

 bed.loadings(x, pc) 

Arguments

x	A bed.matrix
pc	A matrix with Principal Components in columns

Value

A matrix with the corresponding loadings in columns.

Author(s)

Hervé Perdry and Claire Dandine-Roulland

Examples

# load chr2 data set (~10k SNPs in low LD)
x <- read.bed.matrix( system.file("extdata", "chr2.bed", package="gaston") )

# Compute Genetic Relationship Matrix
standardize(x) <- "p"
K <- GRM(x)

# Eigen decomposition
eiK <- eigen(K)
# deal with small negative eigen values
eiK$values[ eiK$values < 0 ] <- 0

# Note: the eigenvectors are normalized, to compute 'true' PCs
# multiply them by the square root of the associated eigenvalues
PC <- sweep(eiK$vectors, 2, sqrt(eiK$values), "*")

# Compute loadings for the 2 first PCs 
# one can use PC[,1:2] instead of eiK$vectors[,1:2] as well
L <- bed.loadings(x, eiK$vectors[,1:2])
dim(L)
head(L)

# the loadings are normalized
colSums(L**2)

# Verify that these are loadings
head( (x %*% L) / sqrt(ncol(x)-1) )
head( PC[,1:2] )

gaston documentation built on Dec. 28, 2022, 1:30 a.m.