makePedigreeFactor: Converts a numeric pedigee to a pedigree with factors

Description

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

Usage

makePedigreeFactor(id, sire, dam, key)

Arguments

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

Value

returns the pedigree with all ids specified as factors according to key

References

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.

Examples

Run this code

# NOT RUN {
## 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)

# }