R: Check a pedigree

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]