Added quantregForest implementation so as to implement confidence intervals
corrections in R/array2seq.R
corrections to R/TT_Params.R
corrected man/train.and.predict.Rd
fixed R/train_and_predict.R to reveal upper and lower quantiles
trying out some stuff with feature selection to accommodate quantregForest's demands
fixed something wrong with train_and_predict.R as well as documentation issues for TT.Seq
corrected documenation file man/TT.Seq.Gene.Rd
added a skip train-and-predict condition: when the number of unique HTS training values are fewer than 5
added another condition to protect quantregForest from too few predictors (<5)
modified TT.Params object; added automatic gene-by-gene tuning for optimal parameters; made comments in README
Major experimental changes: added gene-specific tuning (highly likely to be buggy), fixed a bug in the oob.filter() function
attempt to fix run() and oob.run() arguments
more changes to run(), oob.run() and array2seq() arguments
have a working version of run(), oob.run() and array2seq()
fixed a lot of documentation issues; tried to set 'Not run:... End(Not run)' - we'll see how it goes
added '\dontrun{...}' to man/*.Rd files
delete tuning models immediately to save memory?
added functions to get lower and upper prediction bounds when using quantregForest; added TODO list in README
minor corrections