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, column.quality = 7, strand = "+", ...)
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 some column of info-file) lower than this threshold. |
column.quality |
What column of the info-file provides "quality". Default = 7 os r2; possible values include 6 (average postrior probability). |
strand |
Specification of strand, one of "u" (unknown), "+", "-" or "file".
In the latter case, map-file should contain an extended map (the one
including strand and coding). See options to convert.snp.ped
for details.
|
... |
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") #