convert.snp.mach {GenABEL} | R Documentation |
Converts genotypic data from MACH format to internal genotypic data formated file
convert.snp.mach(pedfile, mapfile, infofile, outfile, quality = 0.9, ...)
pedfile |
File with genotypic data from MACH (geno or mlgeno) |
mapfile |
Name of the map file |
infofile |
Name MACH info-file |
outfile |
Output data file |
quality |
Drop the SNPs with quality (as specified in 6th column of info-file) lower than this threshold. |
... |
Other arguments passed to convert.snp.ped
|
This is a simple script converting the MACH data with convert.snp.ped
,
re-loading data, and filtering the snp.data object based on quality as specified in
MACH info-file
Does not return any value, but writes file with GenABEL raw data
The function does not check if "outfile" already exists, thus it is always over-written
Yurii Aulchenko
load.gwaa.data
,
convert.snp.illumina
,
convert.snp.text
,
convert.snp.ped
,
convert.snp.tped
# # convert.snp.mach(ped="pedin.18",map="map.18",out="genos.raw") #