| makePedigreeNumeric {pedantics} | R Documentation |
Some internal pedantics modules require that pedigrees be
specified only by numerical values, including numerical values
for missing data, this provides that conversion
makePedigreeNumeric(id, sire, dam, missingVal = NULL)
id |
Individual identifiers - pass using as.character() |
sire |
Sire codes - pass using as.character() |
dam |
Dam codes - pass using as.character() |
missingVal |
the indicator that should be substituted for missing values |
numericPedigree |
The factor pedigree in numeric form |
idKey |
A key to facilitate conversion back to the original identifiers |
Michael Morrissey michael.morrissey@ed.ac.uk
Morrissey, M.B, and A.J. Wilson, 2009. pedantics, an R package for pedigree-based genetic simulation, and pedigree manipulation, characterisation, and viewing. Molecular Ecology Resources.
pedigree<-as.data.frame(matrix(c(
"m1", NA, NA,
"m2", NA, NA,
"m3", NA, NA,
"d4", NA, NA,
"d5", NA, NA,
"o6", "m1", "d4",
"o7", "m1", "d4",
"o8", "m1", "d4",
"o9", "m1", "d4",
"o10", "m2", "d5",
"o11", "m2", "d5",
"o12", "m2", "d5",
"o13", "m2", "d5",
"o14", "m3", "d5",
"o15", "m3", "d5",
"o16", "m3", "d5",
"o17", "m3", "d5"),17,3,byrow=TRUE))
names(pedigree)<-c("id","dam","sire")
for(x in 1:3) pedigree[,x]<-as.factor(pedigree[,x])
## make the test pedigree numeric with NAs denoted by -1
makePedigreeNumeric(id=as.character(pedigree[,1]),
dam=as.character(pedigree[,2]),
sire=as.character(pedigree[,3]),
missingVal=-1)