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I'm having an issue with the "selectedPathways" argument in the oncoplot function, when using my own user-defined pathways. I either get the error below (with code):
OR, it works, but the number of samples affected is incorrect. For example, for the pathway "REACTOME_FGFR2_ALTERNATIVE_SPLICING", the results of the "pathways" function indicates that 24 out of 37 samples should be altered. If I take the list of genes in that pathway and provide it as an argument to the oncoplot through the "genes" argument, then I correctly get 24/37. If I provide the pathway name through the "selectedPathways" argument, I instead get 8/37 altered, which seems to be incorrect. Below is all the code and the results I'm getting - would appreciate your help.
I've also attached the pathway data-frame I'm providing as input. I had to switch the order of the Gene and Pathways column, as it seems that the pathways function expects the pathway column first, whereas the oncoplot function expects the gene names first.
Hi,
I'm having an issue with the "selectedPathways" argument in the oncoplot function, when using my own user-defined pathways. I either get the error below (with code):
OR, it works, but the number of samples affected is incorrect. For example, for the pathway "REACTOME_FGFR2_ALTERNATIVE_SPLICING", the results of the "pathways" function indicates that 24 out of 37 samples should be altered. If I take the list of genes in that pathway and provide it as an argument to the oncoplot through the "genes" argument, then I correctly get 24/37. If I provide the pathway name through the "selectedPathways" argument, I instead get 8/37 altered, which seems to be incorrect. Below is all the code and the results I'm getting - would appreciate your help.
I've also attached the pathway data-frame I'm providing as input. I had to switch the order of the Gene and Pathways column, as it seems that the pathways function expects the pathway column first, whereas the oncoplot function expects the gene names first.
reactome_pathways.txt
output with specifying the pathway genes manually
**output with oncoplot pathways function**Thanks for the great package, it's been really helpful for my analysis.
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