Skip to contents

Determine pairwise relatedness

Source: R/statistics.R
relatedness.Rd

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

Value

A data frame of individuals and relatedness score \(A_{jk}\)

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).

Author

Piyal Karunarathne, Klaus Schliep

Examples

vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
relate<-relatedness(vcf)
#> generating table
#> 
  |                                                        
  |                                                  |   0%
  |                                                        
  |=====                                             |  10%
  |                                                        
  |==========                                        |  20%
  |                                                        
  |===============                                   |  30%
  |                                                        
  |====================                              |  40%
  |                                                        
  |=========================                         |  50%
  |                                                        
  |==============================                    |  60%
  |                                                        
  |===================================               |  70%
  |                                                        
  |========================================          |  80%
  |                                                        
  |=============================================     |  90%
  |                                                        
  |==================================================| 100%
#> assessing pairwise relatedness
#> 
  |                                                        
  |                                                  |   0%
  |                                                        
  |                                                  |   1%
  |                                                        
  |=                                                 |   2%
  |                                                        
  |==                                                |   3%
  |                                                        
  |==                                                |   4%
  |                                                        
  |==                                                |   5%
  |                                                        
  |===                                               |   6%
  |                                                        
  |====                                              |   7%
  |                                                        
  |====                                              |   8%
  |                                                        
  |====                                              |   9%
  |                                                        
  |=====                                             |  10%
  |                                                        
  |======                                            |  11%
  |                                                        
  |======                                            |  12%
  |                                                        
  |======                                            |  13%
  |                                                        
  |=======                                           |  14%
  |                                                        
  |========                                          |  15%
  |                                                        
  |========                                          |  16%
  |                                                        
  |========                                          |  17%
  |                                                        
  |=========                                         |  18%
  |                                                        
  |==========                                        |  19%
  |                                                        
  |==========                                        |  20%
  |                                                        
  |==========                                        |  21%
  |                                                        
  |===========                                       |  22%
  |                                                        
  |============                                      |  23%
  |                                                        
  |============                                      |  24%
  |                                                        
  |============                                      |  25%
  |                                                        
  |=============                                     |  26%
  |                                                        
  |==============                                    |  27%
  |                                                        
  |==============                                    |  28%
  |                                                        
  |==============                                    |  29%
  |                                                        
  |===============                                   |  30%
  |                                                        
  |================                                  |  31%
  |                                                        
  |================                                  |  32%
  |                                                        
  |================                                  |  33%
  |                                                        
  |=================                                 |  34%
  |                                                        
  |==================                                |  35%
  |                                                        
  |==================                                |  36%
  |                                                        
  |==================                                |  37%
  |                                                        
  |===================                               |  38%
  |                                                        
  |====================                              |  39%
  |                                                        
  |====================                              |  40%
  |                                                        
  |====================                              |  41%
  |                                                        
  |=====================                             |  42%
  |                                                        
  |======================                            |  43%
  |                                                        
  |======================                            |  44%
  |                                                        
  |======================                            |  45%
  |                                                        
  |=======================                           |  46%
  |                                                        
  |========================                          |  47%
  |                                                        
  |========================                          |  48%
  |                                                        
  |========================                          |  49%
  |                                                        
  |=========================                         |  50%
  |                                                        
  |==========================                        |  51%
  |                                                        
  |==========================                        |  52%
  |                                                        
  |==========================                        |  53%
  |                                                        
  |===========================                       |  54%
  |                                                        
  |============================                      |  55%
  |                                                        
  |============================                      |  56%
  |                                                        
  |============================                      |  57%
  |                                                        
  |=============================                     |  58%
  |                                                        
  |==============================                    |  59%
  |                                                        
  |==============================                    |  60%
  |                                                        
  |==============================                    |  61%
  |                                                        
  |===============================                   |  62%
  |                                                        
  |================================                  |  63%
  |                                                        
  |================================                  |  64%
  |                                                        
  |================================                  |  65%
  |                                                        
  |=================================                 |  66%
  |                                                        
  |==================================                |  67%
  |                                                        
  |==================================                |  68%
  |                                                        
  |==================================                |  69%
  |                                                        
  |===================================               |  70%
  |                                                        
  |====================================              |  71%
  |                                                        
  |====================================              |  72%
  |                                                        
  |====================================              |  73%
  |                                                        
  |=====================================             |  74%
  |                                                        
  |======================================            |  75%
  |                                                        
  |======================================            |  76%
  |                                                        
  |======================================            |  77%
  |                                                        
  |=======================================           |  78%
  |                                                        
  |========================================          |  79%
  |                                                        
  |========================================          |  80%
  |                                                        
  |========================================          |  81%
  |                                                        
  |=========================================         |  82%
  |                                                        
  |==========================================        |  83%
  |                                                        
  |==========================================        |  84%
  |                                                        
  |==========================================        |  85%
  |                                                        
  |===========================================       |  86%
  |                                                        
  |============================================      |  87%
  |                                                        
  |============================================      |  88%
  |                                                        
  |============================================      |  89%
  |                                                        
  |=============================================     |  90%
  |                                                        
  |==============================================    |  91%
  |                                                        
  |==============================================    |  92%
  |                                                        
  |==============================================    |  93%
  |                                                        
  |===============================================   |  94%
  |                                                        
  |================================================  |  95%
  |                                                        
  |================================================  |  96%
  |                                                        
  |================================================  |  97%
  |                                                        
  |================================================= |  98%
  |                                                        
  |==================================================|  99%
  |                                                        
  |==================================================| 100%