gaston: reshape.GRM – R documentation

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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)

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

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

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

v1.5.7

GPL-3

Authors

Hervé Perdry [cre, aut, cph], Claire Dandine-Roulland [aut, cph], Deepak Bandyopadhyay [cph] (C++ gzstream class), Lutz Kettner [cph] (C++ gzstream class)

Initial release

2020-09-18