[BioC] cummerbund how to get matrix for csheatmap

[Valerie Obenchain]

Hi Adrian,

If we follow the example in the vignette we eventually get to these 
lines which I think are similar to what you are showing below.

 From vignette:
...

data(sampleData)
myGeneIds<-sampleIDs
myGeneIds
myGenes<-getGenes(cuff,myGeneIds)
myGenes
head(fpkm(myGenes))
h<-csHeatmap(myGenes,cluster='both')


To get the data plotted in csHeatmap() you'll want to look inside the 
the 'myGenes' object.

 > myGenes
CuffGeneSet instance for  20  genes

Slots:
      annotation
      fpkm
      repFpkm
      diff
      count
      isoforms     CuffFeatureSet instance of size 45
      TSS         CuffFeatureSet instance of size 23
      CDS         CuffFeatureSet instance of size 36
      promoters         CuffFeatureSet instance of size 20
      splicing         CuffFeatureSet instance of size 23
      relCDS         CuffFeatureSet instance of size 20

Each of the slots has an accessor and I think fpkm() is what your are 
looking for.

 > head(fpkm(myGenes))
       gene_id sample_name        fpkm     conf_hi  conf_lo quant_status
1 XLOC_000069 Fibroblasts 2.05083e-01 8.94501e-01 0.000           OK
2 XLOC_000069        hESC 1.77686e+02 2.15888e+02 139.484           OK
3 XLOC_000069         iPS 1.90000e+01 3.88149e+01 0.000           OK
4 XLOC_000089 Fibroblasts 1.39701e+04 2.19187e+04 6021.450           OK
5 XLOC_000089        hESC 7.18339e+03 7.92296e+03 6443.810           OK
6 XLOC_000089         iPS 1.41690e+03 1.96558e+03 868.215           OK
         stdev
1    0.344709
2   19.101000
3    9.907450


Valerie


On 03/01/13 10:05, Adrian Johnson wrote:
> Hi:
> I am trying to plot the most significant genes. I have 3 different
> sample types and 4 replicates each. Could anyone suggest how do I get
> the matrix of fpkm values that was plotted in csHeatmap function.
>
>> diffGeneIDs <- getSig(cuff,level="genes",alpha=0.001)
>> diffGenes<-getGenes(cuff,diffGeneIDs)
>> h<-csHeatmap(diffGenes,cluster='both')
>
> the heatmap gene names are not visible. I want to get the matrix for h
> and plot heatmap using another heatmap function.
> How do I get the matrix for h.
>
> thanks
> Adrian
>
>
>
>
>
>
>
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
>   [1] cummeRbund_2.0.0     Gviz_1.2.1           rtracklayer_1.18.2
> GenomicRanges_1.10.7 IRanges_1.16.6       fastcluster_1.1.8
> reshape2_1.2.2
>   [8] ggplot2_0.9.3        RSQLite_0.11.2       DBI_0.2-5
> BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.20.4   Biobase_2.18.0         biomaRt_2.14.0
>     Biostrings_2.26.3      biovizBase_1.6.2       bitops_1.0-5
>   [7] BSgenome_1.26.1        cluster_1.14.3         colorspace_1.2-1
>     dichromat_2.0-0        digest_0.6.3
> GenomicFeatures_1.10.2
> [13] gtable_0.1.2           Hmisc_3.10-1           labeling_0.1
>     lattice_0.20-13        MASS_7.3-23            munsell_0.4
> [19] parallel_2.15.2        plyr_1.8               proto_0.3-10
>     RColorBrewer_1.0-5     RCurl_1.95-3           Rsamtools_1.10.2
> [25] scales_0.2.3           stats4_2.15.2          stringr_0.6.2
>     tools_2.15.2           XML_3.95-0.1           zlibbioc_1.4.0
>
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