prunePed
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),]
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
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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