Ask help for TCGAnalyze_SurvivalCoxNET function.

Question

[BioLite]

Hi, I'm dealing with TCGA data, but when I visualized my interested genes with TCGAnalyze_SurvivalCoxNET function, I was informed an error by R. Here is my code and error:

TabCoxNet <- TCGAvisualize_SurvivalCoxNET(dataClin,
                                      dataFilt, 
                                      Genelist = rownames(dataSurv),
                                      scoreConfidence = 700,
                                      org.Hs.string = org.Hs.string,
                                      titlePlot = "Case Study n.1 dnet")
Error in `[.data.frame`(x, r, vars, drop = drop) : undefined columns selected

I have noticed that there was a similar post in Github[https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/99], sadly, no any good suggestion was put forward. Maybe someone could solve this today? Any suggestion will be thanked!

[Kevin Blighe]

They appear to not be following up with TCGAbiolinks issues on GitHub (I had even posted one). You may have a quick response from Tiago if you post on Bioconductor forum.

Answer 1

[mhittle]

There are a couple column name issues present and a fix hasn't been merged in Github. Just create a new method in your code and use this code:

https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/147