Converts genotypic data from Illumina/Affymetrix-like format to internal genotypic data formated file
Map + genotypic data file name
Output data file
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.
Reports progress after reading bcast portion of SNP genotypes
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.
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
1 2 3
# # convert.snp.illumina(infile="pedin.18",out="genos.raw",strand="+") #
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