mapReactomeSets mystery object

[arcolombo]

tx.DF and gs, and gn.DF are mystery objects not defined anywhere in this method. probably saved in local envrnmnt during the script creation.

need to re-run the reactome mapping TxDbLite flow.

AC

[ttriche]

ruh roh. the methods work, at least (verified manually after running on
Stanford, TARGET, and TCGA AML RNAseq data)

--t

On Fri, Aug 19, 2016 at 10:15 AM, Anthony R. Colombo <
notifications@github.com> wrote:

tx.DF and gs, and gn.DF are mystery objects not defined anywhere in this
method. probably saved in local envrnmnt during the script creation.

need to re-run the reactome mapping TxDbLite flow.

AC

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[arcolombo]

yes you verified arkas, not txdblite.

need to rebuild something from scratch with TxDbLite.

this is actually the last NOTE that needs to be resolved

[arcolombo]

so I've tested the function reactomeSets which is the right way to formate the cache compatible with qusage. mapReactomeSets.R is not working, and maybe should be deprecated. leaving in for now.