extend {GeneticsPed}R Documentation

Extend pedigree

Description

extend finds ascendants, which do not appear as subjects in pedigree and assigns them as subjects with unknown ascendants in extended pedigree.

Usage

extend(x, ascendant=NULL, col=NULL, top=TRUE)

Arguments

x pedigree object
ascendant character, column names of ascendant(s), see details
col character, column name(s) of attribute(s), see details
top logical, add ascendants as subjects on the top or bottom of the pedigree

Details

Argument ascendant can be used to define, which ascendants will be extended. If ascendant=NULL, which is the default, all ascendant columns in the pedigree are used. The same approach is used with other pedigree attributes such as sex, generation, etc. with argument col. Use col=NA, if none of the pedigree attributes should be extended.

Sex of “new” subjects is infered from attribute ascendantSex as used in Pedigree function. Generation of “new” subjects is infered as minimal (generationOrder="increasing") or maximal (generationOrder="decreasing") generation value in descendants - 1. See Pedigree on this issue. Family values are extended with means of family.

Value

Extended pedigree, where all ascendants also appear as subjects with unknown ascendants and infered other attributes such as sex, generation, etc. if this attributes are in the pedigree.

Author(s)

Gregor Gorjanc

See Also

Pedigree, family, geneticGroups???

Examples

  # --- Toy example ---
  ped <- generatePedigree(nId=5, nGeneration=4, nFather=1, nMother=2)
  ped <- ped[10:20,]
  ped[5, "father"] <- NA # to test robustnes of extend on NA
  extend(ped)
  extend(ped, top=FALSE)

  ## Extend only ascendant and their generation
  extend(ped, col="generation")
  extend(ped, col=c("generation", "sex"))

  # --- Bigger example ---
  ped <- generatePedigree(nId=1000, nGeneration=10, nFather=100,
                          nMother=500)
  nrow(ped)
  # Now keep some random individuals
  ped <- ped[unique(sort(round(runif(n=nrow(ped)/2, min=1,
                                     max=nrow(ped))))), ]
  nrow(ped)
  nrow(extend(ped))

[Package GeneticsPed version 1.0.0 Index]