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MartinFXP / DawnRank

driver gene identification algorithm DawnRank 2014
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How to select the genes like example data #4

Open LiuYangyang-math opened 2 years ago

LiuYangyang-math commented 2 years ago

It's a great work! I have a little question here that I don't understand how you select the "1492 genes" in example BRCA mutation and expression data, but the raw TCGA expression data have thousands genes, I'm confused about this.

MartinFXP commented 2 years ago

Since I did not author this package (I just parallelized it and improved speed in general), I do not know (or remember) how the authors decided for the selected genes. But you can look into the original package page and the publication. The corresponding links are at the bottom of the readme.

LiuYangyang-math commented 2 years ago

Since I did not author this package (I just parallelized it and improved speed in general), I do not know (or remember) how the authors decided for the selected genes. But you can look into the original package page and the publication. The corresponding links are at the bottom of the readme.

Thanks a lot for your reply! I have read the original paper, package manual file and the readme file very carefully, but author didn't mention it. And the method of select genes is important for our work now, we checked a lot of information but no clue, that's why I'm confused about this. I'm very sorry for my rude behavior ,but would you tell me that how to contact the author, I cannot contact the author(the email in the paper is fail), very thanks!

MartinFXP commented 2 years ago

I'm sorry, but I do not have more information than stated in the readme.

In general you do not have to select for genes before using dawnrank. After all dawnrank does the ranking for you. Of course you can select for genes which are differentially expressed between normal and cancer tissue or select genes which have a high variability. Those are standard approaches for gene selection.