function to convert genotypic data from Affymetrix to internal format

convert.snp.affymetrix {GenABEL}R Documentation

function to convert genotypic data from Affymetrix to internal format


Converts genotypic data from Affymetrix format to internal genotypic data formated file


convert.snp.affymetrix(dir, map, outfile, skipaffym)


dir Directory which affymetrix files storages.
map File name with map (annotation) information.
outfile Output data file.
skipaffym Number of lines to skip in the Affymetrix file.


Affymetrix file has following format:

some information...

some information...

some information...

SNPID Call Confidence others column ...

AFFX-7317060 AB 0.01709367 ...

AFFX-7317061 BB 0.01683776 ...

AFFX-7317067 AB 0.01704767 ...

AFFX-7317077 AB 0.01817814 ...

AFFX-7317078 AA 0.0006741961 ...

AFFX-7317079 AA 0.004776776 ...

AFFX-7317063 AB 0.006349149 ...

AFFX-7317064 AB 0.04771883 ...

AFFX-7317067 AA 0.04387166 ...

The first several lines do not contain genotype information and have to be skiped. Skiped numbers of lines can be setted. by setting skipaffym input parameter. For above examle it has to be skipaffym=3.

Every row corresponds to a SNP. The first column is snp name, the second - genotype. The second column can contain letters (AA, AB, BB) or figures (1, 2, 3). Another values consider as unmeasured.

All affymetrix files must have same SNP amount and same SNP order.

The first two lines in the map file will be skiped.

If SNP does not exist in map (annotation) file this SNP will be skiped.

Output will be writen into file pointed in outfile.


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


Maksim Struchalin

See Also, convert.snp.text, convert.snp.mach, convert.snp.tped convert.snp.illumina


## Not run: 
	convert.snp.affymetrix(dir="where_is_our_aff_files", map="map_file", outfile="output.raw", skipaffym=3)

## End(Not run)

[Package GenABEL version 1.6-7 Index]