Question: cummeRbund heatmap for specific isoforms (not genes)
0
gravatar for domenico.somma
2.6 years ago by
domenico.somma0 wrote:

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?

ADD COMMENTlink written 2.6 years ago by domenico.somma0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 229 users visited in the last hour