Plot table with all replicates in cuffdiff output with cummeRbund
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Entering edit mode
9.2 years ago
sindrelee ▴ 10

Hi

Can someone help to do the following from the cummeRbund package:

I only want to plot a simple table by tweaking this command:

gl.iso.rep<-expressionPlot(isoforms(myGene),replicates=T)


Thank you so much

r cufflinks cuffdiff cummerbund plot • 3.9k views
2
Entering edit mode
8.9 years ago
Martombo ★ 3.0k

expressionPlot is not going to produce a table but a line plot, showing the FPKM value of a gene or a feature for each condition of your analysis. if you're interested in plotting isoforms, your command is correct. what you need to do before this is: reading the cuffdiff results (while in the folder with the cuffData.db file) and get your gene(s) of interest from it (as shown in the example below)

cuff=readCufflinks(genome="hg19",gtfFile="human_ref_genes.gtf")
myGene=getGene(cuff,geneId="NM_201574")