inst/examples/example4.md

In pedigreeTools: Versatile Functions for Working with Pedigrees

Example: Pedigree analyses for self-polinated species.

Here we illustrate the use of the function getASelfing in the computation of the A matrix from an example pedigree which contains information on number of selfing cycles (nCycles), and illustrate the differences in the A matrix before and after taking selfing into account.

Section A: Creation of example data.frame pedigrees with and without selfing cycles

Below we create an example pedigree ( identical to the one in Example 1 ) before taking selfing into account.

pedNoCycles <-data.frame(sire=as.character(c(NA,NA,NA,NA,NA,1,3,5,6,4,8,1,10,8)),
                      dam= as.character(c(NA,NA,NA,NA,NA,2,2,NA,7,7,NA,9,9,13)),
                      label=as.character(1:14))

| Subject | Sire | Dam | |----------:|-------------:|------:| | 1 | NA| NA | 2 | NA| NA | 3 | NA| NA | 4 | NA| NA | 5 | NA| NA | 6 | 1| 2 | 7 | 3 | 2 | 8 | 5 | NA | 9 | 6| 7 | 10 | 4| 7 | 11 | 8 | NA | 12 | 1 | 9 | 13 | 10| 9 | 14 | 8| 13

Here we create an example pedigree similar to the one used previously with an additional column called nCycles that takes selfing into account.

Note that this pedigree must be complete and sorted ( see Example 1 )before using it with the functions in Section B.

pedCycles <-data.frame(sire=as.character(c(NA,NA,NA,NA,NA,1,3,5,6,4,8,1,10,8)),
                      dam= as.character(c(NA,NA,NA,NA,NA,2,2,NA,7,7,NA,9,9,13)),
                      label=as.character(1:14),nCycles=c(0,0,0,0,0,0,0,5,0,0,0,0,3,0))

| Subject | Sire (Parent 1) | Dam (Parent 2) | nCycles | |----------:|-------------:|------:|-------:| | 1 | NA| NA | 0| | 2 | NA| NA | 0| | 3 | NA| NA | 0| | 4 | NA| NA | 0| | 5 | NA| NA | 0| | 6 | 1| 2 | 0| | 7 | 3 | 2 | 0| | 8 | 5 | NA | 5| | 9 | 6| 7 | 0| | 10 | 4| 7 | 0| | 11 | 8 | NA | 0| | 12 | 1 | 9 | 0| | 13 | 10| 9 | 3| | 14 | 8| 13 | 0|

Section B: Computation of the additive relationship matrix using the function getASelfing

Here we create the matrix Aself from pedCycles using getAselfing which computes the additive relationship matrix from the pedigree given the information contained in nCycles.

library(pedigreeTools)

Aself <- getASelfing(ID=pedCycles$label,Par1=pedCycles$sire,Par2=pedCycles$dam,nCycles=pedCycles$nCycles,nCyclesDefault=0)

We also create the matrix A from the pedigree before selfing following the method outlined in example 1:

A <- getA(pedNoCycles)

Visualizing the difference matrix of Aself and A shows us that only the members 8,11,13 and 14 are different, as is expected.

diff <- Aself - A
image(diff)

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pedigreeTools documentation built on Aug. 15, 2023, 9:07 a.m.