relatedness: Determine pairwise relatedness

In rCNV: Detect Copy Number Variants from SNPs Data

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,
  parallel = FALSE
)

Arguments

vcf	an imported vcf file in a list using readVCF or a data frame of genotypes generated using hetTgen
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.

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

## Not run: vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
relate<-relatedness(vcf)
## End(Not run)

rCNV documentation built on Sept. 30, 2024, 9:39 a.m.