convert.snp.illumina: function to convert genotypic data from Illumina/Affymetrix...

In GenABEL: genome-wide SNP association analysis

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="+")
#

Example output

Loading required package: MASS
Loading required package: GenABEL.data

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