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waldronlab / TCGAutils

Toolbox package for organizing and working with TCGA data
https://bioconductor.org/packages/TCGAutils
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gistic2RangedSummarizedExperiment #7

Closed lgeistlinger closed 6 years ago

lgeistlinger commented 6 years ago

If you want to make use of the functionality that I've written on getting the original GISTIC2 calls (not the one already mapped to genes) of specified peak type for a specified cancer type - check the gistic2RSE function in here:

https://github.com/waldronlab/subtypeHeterogeneity/blob/master/R/setup_subtype_clonality.R

Feel free to use/modify/extend it in your way or prompt modifications or in case you would like to init a pull request.

LiNk-NY commented 6 years ago

Thanks Ludwig! @lgeistlinger I will look into these. Regards, Marcel

LiNk-NY commented 6 years ago

Thanks Ludwig, @lgeistlinger I have included this function in the package. See d390e3a1af72d1bfaec648d032d5be7e0d946d19