Dear Biostars community,
Greeting, I have questions about the CHASMplus launching in Windows. According to the tutorial (https://chasmplus.readthedocs.io/en/latest/quickstart_opencravat.html), I installed OpenCRAVAT and CHASMplus.
But I'm not sure whether CHASMplus is appropriate for my job or not.
Goal: Calculate the importance of mutation per gene by cancer types from CCLE mutation data.
Input file: CCLE mutation.csv (MAF file format)
Expected result: Mutation importance score per gene by cancer type
NOTE: The attached scores came from the ratio of mutation per cancer type. Row: cancer type; Column: geneID
The first question is "Is CHASMplus proper to cell-line genetic feature?". I know that CHASMplus is based on TCGA and hg38. But Cancer Cell Line Encyclopedia (CCLE) data actually did not come from TCGA and was processed with different reference (hg19). Although I run the CHASMplus with the CCLE dataset, does it give the correct result?
The second question is "How CHASMplus annotate cancer type without cancer-type annotation in the input file?" As you can see, CHASMplus needs only seven types of columns without cancer type annotation. Does it automatically calculate the score from TCGA-PanCancer? Can CHASMplus give the result like the second picture?
The last question is "Is there are any ways for resulting in more than 100,000 variants in CHASMplus?"
There are more than 1,000,000 variants in the CCLE mutation file.
But I counted the error as below:
=> I solved this problem by exporting the result by xlsx file. There are total number of genes with scores.
Also, there is a minor problem exporting to an excel file.
I could not find the button for the download result file.
How can I deal with this problem?
Thank you for reading my question. If anyone knows the solution to this situation, please reply to me.
Best regards,
