gap (version 1.6)

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

Description

A function to prepare pedigrees in post-MAKEPED format

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

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.

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.

Examples

if (FALSE) {
cwd <- getwd()
cs.dir <- file.path(find.package("gap.examples"),"tests","kinship")
setwd(cs.dir)
dir()
makeped("ped7.pre","ped7.ped",0,1,"ped7.lop")
setwd(cwd)
# https://lab.rockefeller.edu/ott/
}