Question: Plotting copy number varation: amplification and deletion data from GISTIC
1
gravatar for missnc
2.8 years ago by
missnc10
missnc10 wrote:

Hi there, 

I have carried out GISTIC on some Agilent 244K tumour data. I now have the G-scores for the regions significantly amplified or deleted across tumour samples. I was hoping to be able to produce a plot like figure 1A in the link below (apologies, I cannot directly put the figure into this question for some reason) from the data - would anyone know of an R-package or anything else that would be helpful in producing something that looks like this?

Many thanks!

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198787/figure/F1/

ADD COMMENTlink modified 2.1 years ago by sophiespo0 • written 2.8 years ago by missnc10

Did you manage to plot it? Would you please share if you did it.

ADD REPLYlink written 2.8 years ago by Chirag Nepal2.1k

Hi Chirag,

Did you produce the plot you want? Did you use an R package or any other tool? Could you please tell something about this. I need same kind of plot. Thank you

ADD REPLYlink written 18 months ago by Bioinfo270

I used GISTIC2 and used the figure from it. I added gene names using illustrator.

ADD REPLYlink written 18 months ago by Chirag Nepal2.1k

Thanks for the reply. I generated a plot like this (Copy number variation plot (R package)) But this doesn't show the genes which copy number gain and loss.

ADD REPLYlink written 18 months ago by Bioinfo270

hi, i want to complete the figures just like above,but my data is not the sequence data but the microarray. what should i do ? please.

ADD REPLYlink written 9 months ago by 182275874690

Hi Missnc,

Did you produce the plot you want? Did you use an R package or any other tool? Could you please tell something about this. I need same kind of plot. Thank you

ADD REPLYlink modified 18 months ago • written 18 months ago by Bioinfo270
0
gravatar for sophiespo
2.1 years ago by
sophiespo0
sophiespo0 wrote:

That's a RAE plot.

The tool is here: http://cbio.mskcc.org/downloads/rae/

The publication is here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003179

The most similar thing I've found is: A: Cnv Visualisation Tools

ADD COMMENTlink written 2.1 years ago by sophiespo0
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