Get genetic kinship.

Estimate kinship from standardised genotypes or read pre-computed kinship file. Standardised genotypes can be obtained via standardiseGenotypes.

getKinship(N, sampleID = "ID_", X = NULL, kinshipfile = NULL,
  id_samples = NULL, standardise = FALSE, sep = ",", header = TRUE,
  verbose = TRUE)

Arguments

N	Number [integer] of samples to simulate.
sampleID	Prefix [string] for naming samples (will be followed by sample number from 1 to N when constructing id_samples).
X	[NrSamples x totalNrSNPs] Matrix of (standardised) genotypes.
kinshipfile	path/to/kinshipfile [string] to be read; either X or kinshipfile must be provided.
id_samples	Vector of [NrSamples] sample IDs [string]; if not provided constructed by paste(sampleID, 1:N, sep="").
standardise	[boolean] If TRUE genotypes will be standardised before kinship estimation.
sep	Field separator [string] of kinship file.
header	[boolean], If TRUE kinship file has header information.
verbose	[boolean]; If TRUE, progress info is printed to standard out

Value

[NrSamples x NrSamples] Matrix of kinship estimate.

Details

The kinship is estimated as \(K = XX_T\), with X the standardised genotypes of the samples. When estimating the kinship from the provided genotypes, the kinship is normalised by the mean of its diagonal elements and 1e-4 added to the diagonal for numerical stability.

Examples

geno <- simulateGenotypes(N=10, NrSNP=50)
#> Simulate 50 SNPs...
K_fromGenotypesNormalised <- getKinship(N=10, X=geno$genotypes,
standardise=TRUE)
#> Standardising the 50 SNPs provided
#> Estimating kinship from 50 SNPs provided
#> Normalising kinship

kinshipfile <- system.file("extdata/kinship",
"kinship.csv",
package = "PhenotypeSimulator")
K_fromFile <- getKinship(N=50, kinshipfile=kinshipfile)
#> Reading kinship file from /private/var/folders/rc/xlxbh6n92qzbm6dh_qqcd56h0000gq/T/RtmpKT8ktk/temp_libpath125b94774d8ae/PhenotypeSimulator/extdata/kinship/kinship.csv