Updates and Release Notes

Release 1.9.4 (2015-05-28)

• RTCGAToolbox has been available on Biocondoctor since 1.9.2
• aaronwolen has implemented the destdir parameter. Users can specify destination directory for permanent data files.

Release 1.3.0 (2015-04-19)

• Two new methods have been added: "getData(FirehoseDataObject,data_type)" will help users to export data from data object. Eg: brcaClinical = getData(brcaObject,"Clinical")
• showResults() function will help users to export toptable or correlation results
• Vignette has been updated
• Some code and internal function updates have been done
• Data objects have been updated. Genes coordinate data has been removed. Now users can use "Homo.sapiens" packet from Bioconductor project for same purpose. Sample code has been provided. Please see vignette or function help ?getReport

Release 1.2.4 (2015-04-10)

• Barcode - UUIDs converter has been implemented. If you set "getUUIDs" parameter as TRUE (default FALSE) on "getFirehoseData" function, RTCGAToolbox gets UUIDs for each barcode that are stored in the return object.

Release 1.2.3 (2015-04-10)

• getFirehoseData function has been updated due to updated connections

Release 1.2.2 (2015-04-04)

• File size limit: Users can set max file size for download. getFirehoseData(fileSizeLimit=500,...

Release 1.2.1 (2015-03-30)

• "show" function has been added for FirehoseData object.

Release 1.2.0 (2015-03-13)

• Client functions has been updated
• All objects are compatible with previous version
• New imports from data.table package
• Vignette has been updated and moved to rmarkdown
• Roxygen meta data has been added
• For methylation data file size control function has been added before download (max limit for gz file set as apprx. 300M)
• Local file function has been added, if you download files one into your workin directory next time tool can reads file from directory without downloading it again (users can overwrite with forceDownload switch)

Release 1.1.2 published (2014-09-15)

• RNASeq, RNASeq2, mRNA_array data matrix structures have been updated.
• New parameter has been added into differentially gene expression function. "meanfilter" parameter can be used to filter raw count matrix. Any row (genes) which median value smaller than "meanfilter" won't be included for analysis.
• Various coding bugs fixed.

Warning: Due to high data volume methylation data may throw warnings or errors.