pedantics (version 1.7)

fixPedigree: Manipulating pedigrees to prepare them for requirements of subsequent analyses

Description

Prepares a pedigree to conform with requirements of many softwares used in quantitative genetic analysis, as well as for many of the functions in pedantics.

Usage

fixPedigree(Ped, dat = NULL)

Arguments

Ped

An ordered pedigree with 3 columns: id, dam, sire

dat

An optional data frame, the same length as the pedigree

Value

Returns a pedigree in which all individuals that exsit in the dam and sire columns are represented by their own record lines, occurring before the records of their first offspring. If data are supplied, then fixPedigree will return a dataframe, the first two columns are the 'fixed' pedigree, and the following columns of which contain appropriately reordered data.

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

# NOT RUN {
##  a valid pedigree, i.e., no loops, no bisexuality, etc.,
## but where not all parents have a record line, and where 
## parents do not necessarily occur before their offspring:
pedigree<-as.data.frame(matrix(c(
  10,1,2,
  11,1,2,
  12,1,3,
  13,1,3,
  14,4,5,
  15,6,7,
  4,NA,NA,
  5,NA,NA,
  6,NA,NA,
  7,NA,NA),10,3,byrow=TRUE))
names(pedigree)<-c("id","dam","sire")
pedigree
fixedPedigree<-fixPedigree(Ped=pedigree)
fixedPedigree
# }