makePedigreeNumeric: Converts a pedigree with individuals specified as factors to a numeric pedigree

Description

Some internal pedantics modules require that pedigrees be specified only by numerical values, including numerical values for missing data, this provides that conversion

Usage

makePedigreeNumeric(id, sire, dam, missingVal = NULL)

Arguments

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

Value

numericPedigree

The factor pedigree in numeric form

idKey

A key to facilitate conversion back to the original identifiers

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 {
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)
# }