al2na/genomation — pull request #38 by frenkiboy (2013-11-08 13:59:17+00:00)
Title: Development

Big changes:
- added test files in the test directory (I took the bigWig test file from the rtracklayer package - so that the stuff now works even on windows)
- test are done for ScoreMatrix, ScoreMatrixList and ScoreMatrixBin - I tested for most of the single parameters and errors, I did not try out all of the possible parameter combinations though
- ScoreMatrixList list now passes all arguments explicitly. I kept the targets instead of target. There was a nasty error if a person put a granges object as a target, and it would be hard to trace it out, so I changed a bit of the parameter testing so that the person is now notified properly if the classes are inappropriate
- removed gffFunctions.R - moved the function to readData.R and changed the code to work directly from a file using readGeneric
- all/most of the functions have examples not - I went through all files twice, but there might have been some that I missed
- some of the examples use your plotting functions, so please use check with --no-examples in this round still, until I make sure all of them work properly
- removed the messages getRandomEnrichment - there were batshit too many