facets-suite
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mskcc
Utility functions for FACETS
Hi Chai Bandlamudi @cband, I found a bug and filed a pull request #38 for it. Please check it out. Useful facets utilities here, hope I helped a little.
In [gene_level_changes.R](https://raw.githubusercontent.com/mskcc/facets-suite/master/R/gene-level-changes.R) > seg = seg[which.max(start-end)], # this selects the segment which represents the larger region it would be nice to add an option to select the segment with the...
https://github.com/mskcc/facets-suite/blob/8a6e3712d8866f1bfb04729247b2f7dca74bd0b9/R/gene-level-changes.R#L111 This line and the next are incorrect. The filters for cf and number of genes on segment are only being applied when the amp is already too big. These...
https://github.com/mskcc/facets-suite/blob/b197695e0328bb81f778af53c3b9682b73c2dcba/annotate-maf-wrapper.R#L107 I'm not sure if it was the version of R but I was getting an error with this version: Error in rbindlist(output_maf, maf[!which(maf$Tumor_Sample_Barcode %in% : Input is data.table but...