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)