R: Error: $ operator not defined for this S4 class when using RadAR package

Question

I am trying to visualize features that were extracted from a dataset of CT-scans using radiomics. I extracted features using the Pyradiomics library, and now I have a few .csv files.

I found this R Library which can read a dataset and generate images for it. Reading the dataset works according to plan using the input = import_pyradiomics(dir = "/path/to/datadir") command, but when I try to visualize it using for instance plot_correlation_matrix(rdr = input, view_as = "heatmap") , one of the visualization functions, I get the following error:

Error: $ operator not defined for this S4 class

I read about S3 and S4 classes, and I think that [ line 160 ] in the library is where this error occurs first as it attempts to call this '$' operator. I am currently using R version 4.0.2. It seems to me like this issue is caused by this R library relying on an older version of R, but it is relatively up to date. What can I do to resolve this issue? Do I have to go in and manually change the code in the library? Or is there an easier fix, such as casting the S4 class to an S3 class? I feel like I'm missing an easy solution because I'm not familiar with R.

I found a similar question here , but it doesn't answer my specific question. Answers on other questions regarding this topic also do not work for me unfortunately.

Answer 1

I am the developer of RadAR, thank you for your interest in our package. The issue was probably related to the use of a different version of the SummarizedExperiment R package. The bug has now been fixed. You can re-install the new version of RadAR from https://github.com/cgplab/RadAR . For any questions related to RadAR, please refer to the "issues" section of the RadAR github page.