Hi,
On Wed, Nov 26, 2008 at 7:46 AM, mortiz <[EMAIL PROTECTED]> wrote:
>
> hi everyone,
>
> i was wondering if there is any function which gives as a result the
> names of the SNPs in their "rs#" form?
this mapping information is available in the Affymetrix NetAffx CSV
files, which you can download from the Affymetrix support page for
each chip type. You find links from the chip type pages on the
aroma.affymetrix site.
An NetAffx CSV file is a large tab-delimited file. Put in under to
corresponding annotationData/ directory and aroma.affymetrix will be
able to find it. Here is an example how to read such files in
aroma.affymetrix:
The pathname of the NetAffx CSV file is:
annotationData/chipTypes/Mapping250K_Nsp/Affymetrix/Mapping250K_Nsp.na26.annot.csv
library("aroma.affymetrix");
chipType <- "Mapping250K_Nsp";
csv <- AffymetrixNetAffxCsvFile$byChipType(chipType, tags=".na26");
print(csv);
AffymetrixNetAffxCsvFile:
Name: Mapping250K_Nsp.na26.annot
Tags:
Pathname:
annotationData/chipTypes/Mapping250K_Nsp/Affymetrix/Mapping250K_Nsp.na26.annot.csv
File size: 426.48MB
RAM: 0.03MB
Number of data rows: NA
Columns [26]: 'probeSetID', 'affySNPID', 'dbSNPRSID', 'chromosome', 'physicalPos
ition', 'strand', 'chrXPseudo-autosomalRegion1', 'cytoband', 'flank', 'alleleA',
'alleleB', 'associatedGene', 'geneticMap', 'microsatellite', 'fragmentEnzymeTyp
eLengthStartStop', 'alleleFrequencies', 'heterozygousAlleleFrequencies', 'number
Ofindividuals/NumberOfChromosomes', 'inHapmap', 'strandVersusdbSNP', 'copyNumber
Variation', 'probeCount', 'chrXPseudo-autosomalRegion2', 'inFinalList', 'minorAl
lele', 'minorAlleleFrequency'
Number of text lines: NA
# We only want to read two of the columns. We use regular expression
to identify
# them by their names, and we read them as "character" strings. Everything else
# will be ignored (the corresponding 'colClasses' will be set to "NULL").
colClassPatterns <- c("(probeSetID|dbSNPRSID)"="character");
df <- readDataFrame(csv, colClassPatterns=colClassPatterns, rows=10:20);
print(df);
probeSetID dbSNPRSID
10 SNP_A-1780611 rs7660291
11 SNP_A-1780610 rs1340013
12 SNP_A-1780415 rs7730126
13 SNP_A-1780576 rs6675133
14 SNP_A-1780413 rs10834942
15 SNP_A-1780412 rs17419765
16 SNP_A-1780574 rs12233450
17 SNP_A-1780379 rs7995987
18 SNP_A-1780572 rs10091369
19 SNP_A-1780378 rs7828844
20 SNP_A-1780377 rs11040883
To read all entries, just drop the 'rows' argument.
Hope this helps
Henrik
>
> thanks!
>
> maria
> >
>
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