Maftools: can't do oncoplot by clinicalfeature
Entering edit mode
3.0 years ago
sunthomas • 0

Hi there,

I am using maftools in RStudio. With the included/example laml maf file I am able to plot an oncoplot and sort by a clinical feature. It works beautifully. Below is the plot I get when I try to sort the data by FAB_classification.

enter image description here

However, when I tried using my own dataset e.g. the pancreatic adenocarcinoma from TCGA, it will give me this error:

> oncoplot(paad, clinicalFeatures = 'grade', sortByAnnotation = TRUE)
Error in strsplit(x = vc.mat, split = ";", fixed = TRUE) : 
  non-character argument

This keeps happening even when I try different maf and clinical files downloaded from TCGA. Does anyone know why?

maftools oncoplot • 2.6k views

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