chkPed {asreml}R Documentation

Check a pedigree

Description

Checks a pedigree for consistency, adds missing founders and sorts so that founders appear before individuals.

Usage

chkPed(
  pedigree,
  fgen = list(character(0), 0.01),
  gender = character(0),
  mv = c("0", "NA"),
  core_version = NULL
)

Arguments

pedigree

A data frame where the first three columns correspond to the identifiers for the individual, male parent and female parent, respectively. Founders or unknown parents use 0 (zero) or NA in the parental columns.

fgen

An optional list of length two where fgen[[1]] is a character string naming the column in pedigree that contains the level of selfing or the level of inbreeding of an individual. In pedigree[,fgen[[1]]], 0 indicates a simple cross, 1 indicates selfed once, 2 indicates selfed twice, etc. A value between 0 and 1 for a base individual is taken as its inbreeding value. If the pedigree has implicit individuals (they appear as parents but not as individuals), they will be assumed base non-inbred individuals unless their inbreeding level is set with fgen[[2]], where 0 < fgen[[2]] < 1 is the inbreeding level of such individuals.

gender

An optional character string naming the column of pedigree that codes for the gender of an individual. pedigree[, gender] is coerced to a factor and must only have two (arbitrary) levels, the first of which is taken to mean "male". An inverse relationship matrix is formed for the X chromosome as described by Fernando and Grossman, 1990 for species where the male is XY and the female is XX.

mv

A character vector of missing value indicators; elements of pedigree that exactly match any of the members of mv are treated as missing. The values passed should be used in addition to "0" and "NA" (default = "0", "NA").

core_version

The version of the algorithmic core to use, not usually required.

Value

The pedigree in a data frame, reordered and expanded if necessary.

[Package asreml version 4.2.0.480 Index]