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.
Arguments
- vcf
an imported vcf file in a list using
readVCF
or a data frame of genotypes generated usinghetTgen
- 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
0.5
(siblings)- verbose
logical. Show progress.
- parallel
logical. Parallelize the process
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.
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
if (FALSE) vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
#> Error: object 'vcf.file.path' not found
relate<-relatedness(vcf) # \dontrun{}
#> Error: object 'vcf' not found