Hi,
library("aroma.affymetrix");
# Get the CDF, which contains the unit names
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
# Get the UGP file, which contains the genomic positions
ugp <- getAromaUgpFile(cdf);
# Extract genomic positions
data <- readDataFrame(ugp);
# Add unit names
rownames(data) <- getUnitNames(cdf);
which gives
> data[1020:1024,]
chromosome position
SNP_A-2001840 1 34306289
SNP_A-4214120 1 34357252
SNP_A-2001896 1 34377866
SNP_A-4268333 1 34436399
SNP_A-2002002 1 34519557
The above works, because all unit-oriented data files, including CDF
and UGP annotation data files, are indexed by units such that unit
#1023 in the CDF corresponds to the same unit in the UGP.
To write this directly to a text file, see how-to page 'Write
annotation data as a tab-delimited text file':
http://aroma-project.org/howtos/annotationData-writeDataFrame
which is even easier.
/Henrik
PS.
On Wed, Dec 29, 2010 at 9:57 PM, Gregory W <greg.d.w...@gmail.com> wrote:
> I should state that I know about the "How tos" section. It seems like
> its still under construction.
>
> And
>
>> ?GenomeInformation
>
> gives some helpful suggestions but at times it can be a little
> overwhelming with all the inherited classes.
>
>
>
>
>
> On Dec 29, 12:43 pm, Gregory W <greg.d.w...@gmail.com> wrote:
>> Hello,
>>
>> I have what I think its a pretty easy question.
>>
>> After reading in the CDF file and getting basic information:
>>
>> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6",
>> > tags="Full")?GenomeInformation
>> > print(cdf)
>>
>> AffymetrixCdfFile:
>> Path: annotationData/chipTypes/GenomeWideSNP_6
>> Filename: GenomeWideSNP_6,Full.cdf
>> Filesize: 470.44MB
>> Chip type: GenomeWideSNP_6,Full
>> RAM: 0.01MB
>> File format: v4 (binary; XDA)
>> Dimension: 2572x2680
>> Number of cells: 6892960
>> Number of units: 1881415
>> Cells per unit: 3.66
>> Number of QC units: 4
>>
>> gi <- getGenomeInformation(cdf)
>> si <- getSnpInformation(cdf)
>>
>> I would like to create a data frame where the rows are the marker
>> names with columns: chromosome and position.
>>
>> For instance:
>>
>> Name Chr Position
>> SNP_A-1 1 50013
>>
>> I'm having a hard time manipulating the above data structures to
>> produce this. I appreciate the discussion board and the site in
>> general. Is there any documentation that helps users explore the data
>> classes produced by aroma?
>>
>> Thanks in advance!
>>
>> Greg
>
> --
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> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
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--
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.
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