Hi. On Thu, Jun 14, 2012 at 11:42 PM, Tommaso Mazza <[email protected]> wrote: > Hi All, > this is a trivial question for sure, but please give me an hint. > > I have data from the chip in object and from a Genome-Wide Human SNP Array > 6.0 - Affymetrix and a GeneChip Human Mapping 250K array. > I would like to get the following information out of their chip information > files and of my data: > > SNP name > Chr > Start > End > ref allele > alt allele
The above information is basically available in the Affymetrix NetAffx tab-delimited files, which you can download from Affymetrix via the corresponding product page for each chip type. For instance, if you have the GenomeWideSNP_6.na31.annot.csv file in annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6.na31.annot.csv (following the Aroma standards, cf. http://aroma-project.org/setup/) you can load it using the Aroma Framework as: > library("aroma.affymetrix"); > chipType <- "GenomeWideSNP_6" > db <- AffymetrixNetAffxCsvFile$byChipType(chipType, tags=".*"); > print(db); AffymetrixNetAffxCsvFile: Name: GenomeWideSNP_6.na31 Tags: Full name: GenomeWideSNP_6.na31 Pathname: annotationData/chipTypes/GenomeWideSNP_6/Affymetrix/GenomeWideSNP_6.na31.annot.csv File size: 1.40 GB (1501563495 bytes) RAM: 0.04 MB Number of data rows: NA Columns [27]: 'probeSetID', 'dbSNPRSID', 'chromosome', 'physicalPosition', 'strand', 'chrXPseudo-autosomalRegion1', 'cytoband', 'flank', 'alleleA', 'alleleB', 'associatedGene', 'geneticMap', 'microsatellite', 'fragmentEnzymeTypeLengthStartStop', 'alleleFrequencies', 'heterozygousAlleleFrequencies', 'numberOfindividuals/NumberOfChromosomes', 'inHapmap', 'strandVersusdbSNP', 'copyNumberVariation', 'probeCount', 'chrXPseudo-autosomalRegion2', 'inFinalList', 'minorAllele', 'minorAlleleFrequency', '%GC', 'oMIM' Number of text lines: NA > colClassPatterns <- c("(ID|chromosome|allele.|)$"="character", > "physicalPosition"="integer"); > data <- readDataFrame(db, colClassPatterns=colClassPatterns, trimQuotes=TRUE); > head(data); probeSetID chromosome physicalPosition alleleA alleleB 1 SNP_A-1780419 1 84875173 A G 2 SNP_A-1780418 5 156390980 C T 3 SNP_A-1780415 5 158729947 A G 4 SNP_A-1780414 9 22976592 A C 5 SNP_A-1780413 11 26300969 A G 6 SNP_A-1780412 5 123078585 C T > tail(data) probeSetID chromosome physicalPosition alleleA alleleB 934963 SNP_A-8662133 4 121395702 A G 934964 SNP_A-8676046 X 49367989 C T 934965 SNP_A-8691917 9 44146701 A G 934966 SNP_A-8713315 6 3052250 A G 934967 SNP_A-8628813 X 49183167 C G 934968 SNP_A-8635786 16 60739638 A T Note that 'allleleA' and 'alleleB' are the two allele variant, but it is not that alleleA is always the (in the population) reference allele and the other is the alternative. I don't know where you can find that information. Hope this helps /Henrik > > Is it possible to get them? > If yes, could you post or convey me to some code? > > Many thanks > Tommaso > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to [email protected] > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
