Fixed a message function call in which the paste function got accidentally included.
The boolean result vector of file.symlink is now directly evaluated and a message gets issued upon an error.
The number of samples and replicates is now stored in vectors, as the values are needed in several places.
Since the standard cummeRbund MDSplot gets difficult to interpret with large replicate numbers, a modified version of the plotting code has been copied here.
Fixed a message where the paste function got accidentally included.
The boolean result vector of file.symlink is now evaluated and a warning issued upon errors.
Each plot is now stored in an object so that both, PDF and PNG files can be written.
R objects are now removed, as soon as they are no longer required.