| relatedness {rCNV} | R Documentation |
Determine pairwise relatedness
Description
Relatedness is determined according to genome-wide relationship assessment of Yang et al. 2010 equation 6, on a per sample basis (with itself and others), using SNPs.
Usage
relatedness(vcf, plot = TRUE, threshold = 0.5, verbose = TRUE)
Arguments
vcf |
an imported vcf file in a list using |
plot |
logical. Whether to plot relatedness of samples against themselves, among themselves and outliers |
threshold |
numerical. A value indicating to filter the individuals of
relatedness among themselves. Default |
verbose |
logical. Show progress. |
Details
According to Yang et al. (2010), out breeding non-related pairs should have a relatedness value of zero while the individual with itself will have a relatedness value of one. Relatedness value of ~0.5 indicates siblings.
Value
A data frame of individuals and relatedness score A_{jk}
Author(s)
Piyal Karunarathne, Klaus Schliep
References
Yang, J., Benyamin, B., McEvoy, B. et al. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42, 565569 (2010).
Examples
vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
relate<-relatedness(vcf)