transmart/Rmodules — pull request #26 by wimvanderlinden (2014-10-29 13:02:33+00:00)
Title: harmonization of rnaseq molecular data types

This pull request (together with a number of pull requests for other tranSMART repositories) is about realizing a harmonization of rnaseq molecular data types allowing both readcounts and normalized readcounts to be supported by tranSMART. Advanced analysis tools, such as 'group test for rnaseq' work on rnaseq molecular data sets consisting of readcount observations for rna transcripts. As part of the analysis pipeline, these readcounts are normalized and used in subsequent processing steps. However, also rnaseq data sets exist, which do not contain readcount observations, but contain normalized readcounts, e.g. rpkm's (reads per kilobase per million) or fpkm's (fragments per kilobase per million). The modifications proposed in these set of pull requests enable tranSMART to handle rnaseq data sets which contain readcounts or normalized readcounts or both. For rnaseq data sets that contain normalized readcounts, advanced analyses tools such as heatmap and clustering algorithms, can be applied. The proposed modifications address uploading of rnaseq data sets (sql procedures and table definitions), high dimensional data retrieval (transmart-core-api & transmart-core-db) and advanced data analyses (Rmodules).

The proposed modifications also address an issue with rnaseq functionality which was introduced by a change in transmart-core-db/src/groovy/org/transmartproject/db/dataquery/highdim/rnaseq/RnaSeqModule.groovy. To resolve that issue the upload procedure for a chromosomal region platform needs to be made aware of whether the chromosomal region platform is going to be used for rnaseq data or acgh data and depending on that, fill in the right value for marker_type in the deapp.de_gpl_info record.