# 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 | Dam | 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 May 2, 2019, 2:09 a.m.