makePedigreeNumeric {pedantics}R Documentation

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

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

Value

numericPedigree The factor pedigree in numeric form
idKey A key to facilitate conversion back to the original identifiers

Author(s)

Michael Morrissey michael.morrissey@ed.ac.uk

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.

See Also

makePedigreeFactor

Examples

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)

[Package pedantics version 1.01 Index]