gaston (version 1.4.9)

reshape.GRM: Reshape a Genetic Relationship Matrix

Description

Reshapes a GRM into a data frame listing relationship of (possibly all) pairs of individuals. Options are provided to specify ranges of relationship values to include or exclude. This is useful in the Quality Control process.

Usage

reshape.GRM(K, include = c(-Inf, +Inf), exclude)

Arguments

K

A symmetric matrix (such as produced by GRM)

include

Range of values to include (default is to include all values)

exclude

Range of values to exclude (default it to exclude nothing)

Value

A data frame with three columns named i, j, k.

Details

The relationship between individuals $i$ and $j$ is the coefficient $k_ij$ in the matrix $K$. The functions lists all pair $i, j$ with $i < j$ and $k_ij$ in the range defined by include and outside the range defined by exclude.

See Also

GRM

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
K <- GRM(x)

# List all pairs if individuals with a relationship above 0.07
pairs <- reshape.GRM(K, exclude = c(-Inf, 0.07))

# Exclude first individual from each such pair
x1 <- x[ -pairs$i, ]