R: Recode a Pedigree

pedRecode {QTLRel} | R Documentation

## Recode a Pedigree

### Description

Prepare a pedigree in a format that is suitable for certain functions

### Usage

    pedRecode(ped, ids, all = TRUE, msg = TRUE)

### Arguments

`ped` | A pedigree, which is a data frame (id, sire, dam, ...). If "sex" is a component, male should be "M", "Male" or 1, and female should be "F", "Female" or 2 (other than 0 and 1). If given, "generation" can be numeric 0, 1, 2, ... or non-numeric "F0", "F1", "F2", ..., which should be in an increasing order. Note: 0 is reserved for unknown `sire`, `dam` or `sex`. If a sire/dam is an inbred founder, its ID should be tagged by character 'i' (e.g. 1i, 2i, etc.).
`ids` | If given, only individuals with `ids` and their ancestors are kept in the recoded pedigree.
`all` | If false, sires and dams with no parents are treated as unknown.
`msg` | If false, messages are suppressed.

### Details

This function is used in `cic`, and it can be used for error checking with respect to sex and generation if sex and/or generation information is available. The actual values of generation can be anything but should correspond to the true order of generation; otherwise, `cic` may fail or we may get incorrect results. Information except `id`, `sire` and `dam` is optional.

### Value

A recoded pedigree.

### See Also

`cic`.

### Examples

    data(miscEx)

    pedF8[1:10,]
    pedR<- pedRecode(pedF8)
    pedR[1:10,]
    dim(pedR)
    pedR<- pedRecode(pedF8, ids=pedF8$id[pedF8$gener=="F8"])
    dim(pedR)

[Package QTLRel version 1.0 Index]