[BioC] info on vennCounts function

[James W. MacDonald]

Hi Alberto,

On 6/21/2011 12:53 PM, Alberto Goldoni wrote:
> Dear all,
> i have a question on the "vennCounts" function.
>
> Using this function on "results" value:
>
>> vennCounts(results)
>       [hda+str]-[ref] [ref+str]-[ref] [hda+str]-[ref+str] Counts
> [1,]               0               0                   0             21496
> [2,]               0               0                   1                0
> [3,]               0               1                   0               12
> [4,]               0               1                   1                  0
> [5,]               1               0                   0                32
> [6,]               1               0                   1                  1
> [7,]               1               1                   0                34
> [8,]               1               1                   1                 0
> attr(,"class")
> [1] "VennCounts"
>
> what i shoul need is a way to understand which genes are in the [7,]
> line from the  "[hda+str]-[ref] vs [ref+str]-[ref]".
>
> The only think i know is the number that should be 34, but i would
> like to obtain a list of the 34 genes.

You will need to use the results object to do that. The results object 
will be a matrix with three columns and as many rows as genes in your 
comparison. So e.g., the first column will represent the [hda+str]-[ref] 
comparison, and will consist of 1's, 0's and -1's.

If you do something like

sum(abs(results[,1]) == 1 & abs(results([,2]) == 1)

you should get 34. Given that information, I leave it to you to figure 
out how to subset your genes.

Best,

Jim


>
> best regards.
>
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] AnnotationDbi_1.14.1  Biobase_2.12.1        GenomicFeatures_1.4.2
> [4] GenomicRanges_1.4.1   IRanges_1.10.0        limma_3.8.1
> [7] biomaRt_2.8.0
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.20.0  BSgenome_1.20.0    DBI_0.2-5          RCurl_1.5-0
> [5] RSQLite_0.9-4      rtracklayer_1.12.3 tools_2.13.0       XML_3.2-0
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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