save R objects as RDS

[ChristopherBarrington]

In the results directory, there are RData files, provided from the DESeq2 script. The objects are loaded into a workspace with load so will overwrite any existing similarly named variable and requires the user to know what the variable(s) in the DESeq script were called.

It may be more user-friendly to use an RDS object instead so that it can be read into any variable, independently of its original name in the DESeq script. As far as I can see, this would only apply to the two files/objects below, though I haven't used any quantification methods than rsem.

results/star_rsem/deseq2_qc/deseq2.dds.RData
results/star_rsem/deseq2_qc/size_factors/deseq2.size_factors.RData

[drpatelh]

Ping @macroscian . If you guys fancy coming up with a fix in the next couple of days it will be in the next release.