genetics: write.pop.file – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

write.pop.file

Create genetics data files

Description

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

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

write.marker.file creates a 'marker' data file, as used by the QTDT software package (http://csg.sph.umich.edu//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 https://genepop.curtin.edu.au/help_input.html, the format of 'pedigree' files is documented at http://csg.sph.umich.edu/abecasis/GOLD/docs/pedigree.html and the format of 'marker' files is documented at http://csg.sph.umich.edu/abecasis/GOLD/docs/map.html.

Value

No return value.

Author(s)

Gregory R. Warnes greg@warnes.net

Examples

# TBA

genetics

Population Genetics

v1.3.8.1.3

GPL

Authors

Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch, and Michael Man.

Initial release

2012-11-26