| makePedigreeFactor {pedantics} | R Documentation |
Some internal pedantics modules require that pedigrees be
specified only by numerical values, including numerical values
for missing data, this converts them back to factors
makePedigreeFactor(id, sire, dam, key)
id |
Numeric individual identifiers |
sire |
Numeric sire codes |
dam |
Numeric dam codes |
key |
A dataframe, as produced by makePedigreeNumeric, specifying factor codes for numeric values in is, sire, and dam |
returns the pedigree with all ids specified as factors according to key
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.
## first we'll implement the example from makePedigreeNumeric(),
## and use makePedigreeFactor() to turn it back again:
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
test<-makePedigreeNumeric(id=as.character(pedigree[,1]),
dam=as.character(pedigree[,2]),
sire=as.character(pedigree[,3]),
missingVal=-1)
test$numericPedigree
test$idKey
## and turn it back again
makePedigreeFactor(id=test$numericPedigree$id,
dam=test$numericPedigree$dam,
sire=test$numericPedigree$sire,
key=test$idKey)