CKMRsim-pairwise-relationships

CKMRsim is all about inference of pairwise relationships from genetic data. This vignette documents the named pairwise relationships that come “pre-loaded” with CKMRsim. By saying that they are “pre-loaded” we mean that each relationship’s IBD coefficients are included in the package’s kappa matrix and that the pedigree specifying the relationship (for simulating linked markers) is included in the pedigrees list. Both kappas and pedigrees are included as part of the built-in data for this package.

First, we shall print out a table of the identify coefficients for the different relationships.

library(CKMRsim)
library(tibble)
library(dplyr)
library(stringr)

long_names <- c(
  MZ = "Monozygotic (identical) twins",
  PO = "Parent-offspring",
  FS = "Full siblings",
  HS = "Half siblings",
  GP = "Grandparent-grandchild",
  AN = "Aunt-niece",
  DFC = "Double first cousins",
  HAN = "Half aunt-niece",
  FC = "First cousins",
  HFC = "Half first cousins",
  DHFC = "Double half first cousins",
  SC = "Second cousins",
  HSC = "Half second cousins",
  U = "Unrelated"
)

rtable <- as_tibble(kappas) %>%
  mutate(
    abbreviation = rownames(kappas),
    relationship = long_names
    ) %>%
  select(relationship, abbreviation, everything())

rtable
#> # A tibble: 14 × 5
#>    relationship                  abbreviation kappa0 kappa1 kappa2
#>    <chr>                         <chr>         <dbl>  <dbl>  <dbl>
#>  1 Monozygotic (identical) twins MZ            0     0      1     
#>  2 Parent-offspring              PO            0     1      0     
#>  3 Full siblings                 FS            0.25  0.5    0.25  
#>  4 Half siblings                 HS            0.5   0.5    0     
#>  5 Grandparent-grandchild        GP            0.5   0.5    0     
#>  6 Aunt-niece                    AN            0.5   0.5    0     
#>  7 Double first cousins          DFC           0.562 0.375  0.0625
#>  8 Half aunt-niece               HAN           0.75  0.25   0     
#>  9 First cousins                 FC            0.75  0.25   0     
#> 10 Half first cousins            HFC           0.875 0.125  0     
#> 11 Double half first cousins     DHFC          0.766 0.219  0.0156
#> 12 Second cousins                SC            0.938 0.0625 0     
#> 13 Half second cousins           HSC           0.969 0.0312 0     
#> 14 Unrelated                     U             1     0      0

And now we will show a series pedigrees that depict the relationships, (except for monozygous twins and unrelated, which don’t yield interesting pedigrees) alongside the IBD coefficient values. In these pedigrees, the nodes corresponding to members of the pair are shaded (gray) and are labeled 1 and 2.

Due to the way output files from Mendel are parsed. It is necessary that the members of the pair not be founders in the pedigree. This is why the pedigrees for GP and PO have founders above the oldest members of the pair.