gap (version 1.3-1)

makeped: 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.

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).

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.

Details

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.

Examples

if (FALSE) {
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)
}