write.pop.file: Create genetics data files

In kindlychung/genetics: Population Genetics

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 [e-mail]

See Also

write.table

Examples

  # TBA

kindlychung/genetics documentation built on May 20, 2019, 9:58 a.m.