[BioC] Parsing values from DGEExact$table (created via edgeR)

[James W. MacDonald]

Hi KJ Lim,

On 8/21/2012 9:43 AM, KJ Lim wrote:
> Dear R and edgeR community,
>
> Good day.
>
> I have a question about parsing values from table. I have an R object,
> *ps*which contained a set of tags let's say "AS123645", "AF239456",
> "AG324567"
> and so on.

If you are having questions about simple things like subsetting 
matrices, I would highly recommend reading 'An Introduction to R', which 
comes with R. You can get to it by typing

help.start()

at an R prompt, and then choosing the 'Manuals' link.

You won't get very far without knowing how to do simple manipulations 
like this. For now, please note that you can subset matrices in numerous 
ways, one of which is by passing a character vector of the row names:

subtable <- DGEExact$table[c("AS123645","AF239456", "AG324567"),]

Best,

Jim
>
> I would like to parse the reading which match to tags in the *ps* from a *
> DGEExact$table*. The DGEExact$table is generated with *edgeR* when
> performed the *exactTest* for the RNA-Seq data.
>
> The *DGEExact$table* is looks like:
>
>    An object of class "DGEExact"
>    $table
>                  logFC    logCPM     PValue
>    AA556146  0.3700360 0.6844266 0.86258137
>    AA556148 -0.6134484 3.7174273 0.09524158
>    AA556155  0.3467066 1.7382440 0.63816061
>    58029 more rows ...
>
>
> Could someone kindly please advice me?
>
> Thank you very much.
>
> Best regards,
> KJ Lim
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099