inst/examples/example3.md

In Rpedigree/pedigreeTools: Versatile Functions for Working with Pedigrees

Example 3: Subsetting a Pedigree using prunePed

Section A : Creating the example pedigree and Scrambling it.

Following the previous examples, we start with a scarmbled version of the example data frame pedigree pedFrame

#Creating the example pedigree
pedFrame<-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))
#Scrambling the example pedigree:
pedScram<- pedFrame[sample(replace=FALSE, 1:14),] 

Section B: Using prunePed to subset the pedigree.

The prunePED function works by setting a baseline population through a vector of ids, and the number of previous generations ( sires , dams, grandsires and granddams etc. of the baseline population ) the user wishes to select. Here the number of previous generations to select is set through the ngen argument of prunePED. This selection ends where the parents are unknown regardless of ngen.

Here we start with an example baseline population vector (selectVector) : c(12,9,11) And an ngen value 2

It can be readily seen from the following pictoral representation of the pedigree that the ids that should be returned along with c(12,9,11) are c(1,2,3,5,6,7,8)

# Applying prunePed to subset the scrambled pedigree 
library(pedigreeTools)
pedSelect <- prunePed(pedScram,selectVector=c(12,9,11),ngen=2) 

pedSelect
    sire dam label
 1:   NA  NA     1
 2:    6   7     9
 3:    3   2     7
 4:    1   2     6
 5:    5  NA     8
 6:   NA  NA     3
 7:   NA  NA     2
 8:   NA  NA     5
 9:    1   9    12
10:    8  NA    11

Section C: Producing a valid pedigree object from the output of prunePED

Following Example 1, we create a sorted and complete pedigree object pedFinal that can be used for fitting models from the output of prunePED.

pedEdited <- editPed(sire=pedSelect$sire,dam=pedSelect$dam,label=pedSelect$label)
pedFinal <- with(pedEdited, pedigree(label=label,sire=sire,dam=dam))

 pedFinal
   sire  dam
1  <NA> <NA>
3  <NA> <NA>
2  <NA> <NA>
5  <NA> <NA>
7     3    2
6     1    2
8     5 <NA>
9     6    7
11    8 <NA>
12    1    9

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Rpedigree/pedigreeTools documentation built on Oct. 13, 2023, 9:49 p.m.