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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