Last data update: 2014.03.03
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R: Create genetics data files
write.pop.file | 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
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file |
Output filename
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digits |
Number of digits to use in numbering genotypes, either 2
or 3.
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description |
Description to use as the first line of the 'pop'
file.
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family, pid, father, mother |
Vector of family, individual,
father, and mother id's, respectively.
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sex |
Vector giving the sex of the individual (1=Make, 2=Female)
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location |
Location of the marker relative to the gene of
interest, in base pairs.
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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 greg@warnes.net
See Also
write.table
Examples
# TBA
Results
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