inst/examples/example1.md

In pedigreeTools: Versatile Functions for Working with Pedigrees

Example 1: Completing & sorting a pedigree

A valid pedigree object is a pedigree that is : Complete : Any individual that appears as ancestor must also appear as a row in the Pedigree. Sorted : Ancestors must preceed progeny in the Pedigree. * Formal Class : It is an S4 object of formal class 'Pedigree'. ( See Section B )

The function editPed() can be used to complete and sort pedigrees. In the following example we use the small pedigree printed below to illustrate the use of the function editPed() in the creation of a valid pedigree object from an incomplete and scrambled pedigree.

| 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

Section A : Scrambling the above pedigree and rendering it incomplete.

Here is some example code that : Creates an incomplete version of the pedigree by omitting rows that correspond to four of the five 1st generation parents. Scrambles the incomplete Pedigree.

        ## Create incomplete version of example pedigree 
        PedInc <- data.frame(sire=as.character(c(NA,1,3,5,6,4,8,1,10,8)),
                  dam= as.character(c(NA,2,2,NA,7,7,NA,9,9,13)),
                  label=as.character(5:14))

        ## Scramble incomplete pedigree
        PedScram <- PedInc[sample(replace=FALSE, 1:10),] 

Section B : Reconstructing the complete, sorted pedigree and converting it into a valid 'Pedigree' object

Below is some more example code that : Completes and sorts the incomplete pedigree using editPed and returns a DataFrame. Uses the function pedigree to convert the data frame representation into an S4 object of formal class 'Pedigree'.

        library(pedigreeTools)

        ## Complete and sort incomplete Pedigree using editPed
        PedEdit<- editPed(sire=PedScram$sire, dam= PedScram$dam, label=PedScram$label) 

        ## Converted the data frame PedEdit into an S4 object of formal class 'Pedigree'
        PedFinal<- with(PedEdit, pedigree(label=label, sire=sire, dam=dam))

The object PedFinal is a valid pedigree object that can be used for further analysis with PedigreeTools and pedigreemm. This is what it should look like for this example :

PedFinal

   sire  dam
1  <NA> <NA>
2  <NA> <NA>
3  <NA> <NA>
4  <NA> <NA>
5  <NA> <NA>
7     3    2
8     5 <NA>
6     1    2
11    8 <NA>
9     6    7
10    4    7
13   10    9
12    1    9
14    8   13

str(PedFinal)

Formal class 'pedigree' [package "pedigreeR"] with 3 slots
  ..@ sire : int [1:14] NA NA NA NA NA 3 5 1 7 8 ...
  ..@ dam  : int [1:14] NA NA NA NA NA 2 NA 2 NA 6 ...
  ..@ label: chr [1:14] "1" "2" "3" "4" ...

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