R: A function to prepare pedigrees in post-MAKEPED format

makeped {gap} | R Documentation

## A function to prepare pedigrees in post-MAKEPED format

### Description

Many computer programs for genetic data analysis requires pedigree data to be in the so-called “post-MAKEPED” format. This function performs this translation and allows for some inconsistences to be detected.

The first four columns of the input file contains the following information:

pedigree ID, individual ID, father's ID, mother's ID, sex

Either father's or mother's id is set to 0 for founders, i.e. individuals with no parents. Numeric coding for sex is 0=unknown, 1=male, 2=female. These can be followed by satellite information such as disease phenotype and marker information.

The output file has extra information extracted from data above.

### Usage

    makeped(pifile="pedfile.pre", pofile="pedfile.ped", auto.select=1,
           with.loop=0, loop.file=NA, auto.proband=1, proband.file=NA)

### Arguments

`pifile` | input filename
`pofile` | output filename
`auto.select` | no loops in pedigrees and probands are selected automatically? 0=no, 1=yes
`with.loop` | input data with loops? 0=no, 1=yes
`loop.file` | filename containing pedigree id and an individual id for each loop, set if with.loop=1
`auto.proband` | probands are selected automatically? 0=no, 1=yes
`proband.file` | filename containing pedigree id and proband id, set if auto.proband=0 (not implemented)

### Details

Before invoking makeped, input file, loop file and proband file have to be prepared.

By default, auto.select=1, so translation proceeds without considering loops and proband statuses. If there are loops in the pedigrees, then set auto.select=0, with.loop=1, loop.file="filespec".

There may be several versions of makeped available, but their differences with this port should be minor.

### Value

All output will be written in pofile

### Note

adapted from makeped.c by W Li and others

### Source

http://linkage.rockefeller.edu

### Examples

    ## Not run:
    cwd <- getwd()
    cs.dir <- file.path(path.package("gap.datasets"),"tests","kinship")
    setwd(cs.dir)
    dir()
    makeped("ped7.pre","ped7.ped",0,1,"ped7.lop")
    setwd(cwd)

    ## End(Not run)

[Package gap version 1.2.2 Index]