write.pop.file {genetics}R Documentation

Create genetics data files

Description

write.pop.file creates a 'pop' data file, as used by the GenePop (http://wbiomed.curtin.edu.au/genepop/) and LinkDos (http://wbiomed.curtin.edu.au/genepop/linkdos.html) software packages.

write.pedigree.file creates a 'pedigree' data file, as used by the QTDT software package (http://www.sph.umich.edu/statgen/abecasis/QTDT/).

write.marker.file creates a 'marker' data file, as used by the QTDT software package (http://www.sph.umich.edu/statgen/abecasis/QTDT/).

Usage

write.pop.file(data, file = "", digits = 2, description = "Data from R")
write.pedigree.file(data, family, pid, father, mother, sex,
                    file="pedigree.txt")
write.marker.file(data, location, file="marker.txt")

Arguments

data Data frame containing genotype objects to be exported
file Output filename
digits Number of digits to use in numbering genotypes, either 2 or 3.
description Description to use as the first line of the 'pop' file.
family, pid, father, mother Vector of family, individual, father, and mother id's, respectively.
sex Vector giving the sex of the individual (1=Make, 2=Female)
location Location of the marker relative to the gene of interest, in base pairs.

Details

The format of 'Pop' files is documented at http://wbiomed.curtin.edu.au/genepop/help_input.html, the format of 'pedigree' files is documented at http://www.sph.umich.edu/csg/abecasis/GOLD/docs/pedigree.html and the format of 'marker' files is documented at http://www.sph.umich.edu/csg/abecasis/GOLD/docs/map.html.

Value

No return value.

Author(s)

Gregory R. Warnes warnes@bst.rochester.edu

See Also

write.table

Examples

  # TBA

[Package genetics version 1.3.4 Index]