cummeRbund heatmap for specific isoforms (not genes)
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@domenicosomma-12703
Last seen 11 months ago

Hi,

I have done my RNA-seq analysis, I'm new about R and I am trying to have a heatmap with all the differential expressed genes. With some tutorials and cummeRbund I can create the heatmap for the gene's isoforms (here the code I used, for example)

> myGeneIds<- c("IL8","RELB","TNF")
> myGenes <- getGenes(cuff_data,myGeneIds)
Getting gene information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting isoforms information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting CDS information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting TSS information:
    FPKM
    Differential Expression Data
    Annotation Data
    Replicate FPKMs
    Counts
Getting promoter information:
    distData
Getting splicing information:
    distData
Getting relCDS information:
    distData
Warning messages:
1: Closing open result set, pending rows
2: Closing open result set, pending rows

> h<-csHeatmap(isoforms(myGenes),cluster="row")
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables

> h

The problem is: I don't want plot ALL the gene's isoforms, but only specific isoforms, for example for IL8 only transcript_id NM_0000001, for TNF only NM_0000002...

is it possible?

cummerbund heatmap isoforms transcript_id • 915 views
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