Description Usage Arguments Details Value Examples
This function helps to prepare a pedigree to generate a pedigree object
1 | editPed(sire, dam, label, verbose)
|
sire |
a vector (with some |
dam |
similarly as |
label |
a vector with the subjects id. Giving a unique ID for the corresponding
entry. The length as |
verbose |
logical entry inquiring whether to print line that the program is evaluating. The default is FALSE. |
The function takes a vector of sires, another for dams and a final one for subjects
all of the same length, convert them to character. If there are dams or sires not
declared as subjects the function generates them. Finally, it orders the pedigree.
The output can be used to build a pedigree object ped
A data frame with strings as characters. All subjects are in the label column, and all subjects will appear in this column before appering as sires or dams.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | #(1)
pede<-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))
#scrambled original pedigree:
(pede<- pede[sample(replace=FALSE, 1:14),] )
(pede<- editPed(sire=pede$sire, dam= pede$dam, label=pede$label))
ped<- with(pede, pedigree(label=label, sire=sire, dam=dam))
#################################################################################################
#(2) With missing labels
pede<-data.frame(sire=as.character(c(NA,1,3,5,6,4,8,1,10,8)),
dam= as.character(c(NA,2,2,NA,7,7,NA,9,9,13)),
label=as.character(5:14))
#scrambled original pedigree:
(pede<- pede[sample(replace=FALSE, 1:10),] )
(pede<- editPed(sire=pede$sire, dam= pede$dam, label=pede$label))
ped<- with(pede, pedigree(label=label, sire=sire, dam=dam))
#################################################################################################
#(2) A larger pedigree
#Useing pedCows pedigree
# str(pedCows)
# pede<-data.frame(id=pedCows@label, sire=pedCows@sire, dam=pedCows@dam)
# pede<-pede[sample(1:nrow(pede),replace=FALSE),]
# pede<- editPed(sire=pede$sire, dam=pede$dam, label=pede$id)
# ped<- with(pede, pedigree(label=label, sire=sire, dam=dam))
|
Loading required package: lme4
Loading required package: Matrix
sire dam label
4 <NA> <NA> 4
11 8 <NA> 11
5 <NA> <NA> 5
7 3 2 7
10 4 7 10
2 <NA> <NA> 2
12 1 9 12
13 10 9 13
8 5 <NA> 8
9 6 7 9
6 1 2 6
1 <NA> <NA> 1
3 <NA> <NA> 3
14 8 13 14
label sire dam gene
1 4 <NA> <NA> 0
3 5 <NA> <NA> 0
6 2 <NA> <NA> 0
12 1 <NA> <NA> 0
13 3 <NA> <NA> 0
4 7 3 2 1
9 8 5 <NA> 1
11 6 1 2 1
2 11 8 <NA> 2
5 10 4 7 2
10 9 6 7 2
7 12 1 9 3
8 13 10 9 3
14 14 8 13 4
sire dam label
7 8 <NA> 11
1 <NA> <NA> 5
8 1 9 12
9 10 9 13
3 3 2 7
4 5 <NA> 8
5 6 7 9
6 4 7 10
2 1 2 6
10 8 13 14
label sire dam gene
1 1 <NA> <NA> 0
2 2 <NA> <NA> 0
3 3 <NA> <NA> 0
4 4 <NA> <NA> 0
6 5 <NA> <NA> 0
9 7 3 2 1
10 8 5 <NA> 1
13 6 1 2 1
5 11 8 <NA> 2
11 9 6 7 2
12 10 4 7 2
7 12 1 9 3
8 13 10 9 3
14 14 8 13 4
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