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)
Herv<c3><83><c2><a9> 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, ]