R: function to convert genotypic data from Illumina/Affymetrix...

convert.snp.illumina {GenABEL} | R Documentation

## function to convert genotypic data from Illumina/Affymetrix to internal format

### Description

Converts genotypic data from Illumina/Affymetrix-like format to internal genotypic data formated file

### Usage

    convert.snp.illumina(infile, outfile, strand = "+", bcast = 10000000)

### Arguments

`infile` | Map + genotypic data file name
`outfile` | Output data file
`strand` | Specification of strand, one of "u" (unknown), "+", "-" or "file". In the latter case, extra column specifying the strand (again, one of "u", "+", or "-") should be included on the infile.
`bcast` | Reports progress after reading bcast portion of SNP genotypes

### Details

Input file is the one which could be typically obtained from Illumina BeadStudio software. For example:

Name Chr Pos id1 id2 id3

rs1001 2 12897 AC AA AA

rs2401 3 12357 AG GG AG

rs123 3 5327 TC TT CC

Here, every row corresponds to a SNP, and each column, starting with the 4th, corresponds to a person.

When strand information is available (option strand="file"), the file should look like

Accepted allele codes: 1/2, A/B, A/T, A/G, A/C, T/G, T/C, G/C, A/-, T/-, G/-, C/-. Here, "-" stands of a deletion. Missing data can be coded as "–" or "00". Make sure that the coding for missing is "00" if you use one of the codings A/-, T/-, G/-, C/-!

Name Chr Pos Strand id1 id2 id3

rs1001 2 12897 + AC AA AA

rs2401 3 12357 - AG GG AG

rs123 3 5327 + TC TT CC

Accepted strand coding: +, -, u (unknown)

The procedure always codes genotypes that "0", "1" and "2" correspond to AA, AB, and BB, where B is the less frequent allele. Thus GWA analysis procedures will return effect of the minor allele.

### 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)

Yurii Aulchenko

### See Also

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

### Examples

    #
    # convert.snp.illumina(infile="pedin.18",out="genos.raw",strand="+")
    #

[Package GenABEL version 1.8-0 Index]