reshape.GRM: Reshape a Genetic Relationship Matrix

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

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)

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.

Value

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

Author(s)

Hervé Perdry and Claire Dandine-Roulland

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, ]

gaston documentation built on May 29, 2024, 7:33 a.m.