convert.snp.affymetrix: function to convert genotypic data from Affymetrix to...

In GenABEL: genome-wide SNP association analysis

Description

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

Usage

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

Arguments

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.

Details

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.

Value

Does not return any value, but writes file with GenABEL raw data

Note

The function does not check if "outfile" already exists, thus it is always over-written

Author(s)

Maksim Struchalin

See Also

load.gwaa.data, convert.snp.text, convert.snp.mach, convert.snp.tped convert.snp.illumina

Examples

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

## End(Not run)

GenABEL documentation built on May 30, 2017, 3:36 a.m.