write.pop.file {genetics}

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 [e-mail]

See Also

write.table

Examples

  # TBA