Plot table with all replicates in cuffdiff output with cummeRbund
1
1
Entering edit mode
8.1 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 • 3.7k views
ADD COMMENT
2
Entering edit mode
7.8 years ago
Martombo ★ 2.9k

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")

then your command will work

ADD COMMENT

Login before adding your answer.

Traffic: 1623 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6