[BioC] cummerbund how to get matrix for csheatmap
Adrian Johnson
oriolebaltimore at gmail.com
Fri Mar 8 15:38:09 CET 2013
Thank you Valerie and Loyal. That was helpful.
Adrian
On Tue, Mar 5, 2013 at 11:24 PM, Loyal Goff <lgoff at csail.mit.edu> wrote:
> To follow up, there also exists an fpkmMatrix() method to reshape the fpkm results into a feature X condition matrix, e.g.:
>
> fpkmMatrix(myGenes)
>
> Cheers,
> Loyal
>
> On Mar 5, 2013, at 11:17 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:
>
>> 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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>>
>
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