makePedigreeFactor: Converts a numeric pedigee to a pedigree with factors

In pedantics: Functions to Facilitate Power and Sensitivity Analyses for Genetic Studies of Natural Populations

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

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

Value

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

Author(s)

Michael Morrissey [e-mail]

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

makePedigreeNumeric

Examples

## 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)

pedantics documentation built on May 1, 2019, 10:54 p.m.