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.
A symmetric matrix (such as produced by
Range of values to include (default is to include all values)
Range of values to exclude (default it to exclude nothing)
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
A data frame with three columns named
Herv<c3><a9> Perdry and Claire Dandine-Roulland
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# temporarily set nb threads to 2 to comply with CRAN rules n.threads <- getNumThreads() setThreadOptions(2) # 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, ] # back to previous nb threads value setThreadOptions(n.threads)
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