made a S4 class to define an aldex.clr type
added Methods to Depends in DESCRIPTION
added SummarizedExperiment functionality -- NOT TESTED
made version number 0.99.2, coded up usage of BiocParallel (NOT TESTED)
debugged overloading of aldex.clr class so that it takes in SummarizedExperiment or data frame for the read count table
debugged BiocParallel multi core option (names of data structures were not preserved with bplapply)
fixed documentation, R BUILD and R CHECK work great, even with vignettes. We're missing a vignette PDF.
Merge pull request #2 from ruthgrace/master

Implemented Bioconductor suggestions