al2na/genomation — pull request #52 by frenkiboy (2013-11-15 11:32:09+00:00)
Title: Big one updated

- corrected the show for annotate functions (got broken when cat got replaced with message)
- annotateWithFeature - feature name taken by default from the variable name (if the person calls the function with feature=cpgi, and does not set the feature name, it will be cpgi by default)
- plotGeneAnnotation - rewritten it - now works, changed the name from plotGenicAnnotation
- changed the class names
randomEnrichment -> RandomEnrichment
annotationByFeature -> AnnotationByFeature
annotationByGenicParts -> AnnotationByGeneParts

- annotateWithFeatureFlank and annotateWithFeature:
- changed the feature argument to target

- added interxect.chr argument to all annotation functions
- changed the GRangeLinst.obj argument to feature

- moved the class definition from readAnnotate.R to genomation-classes.R
- scoreMatrixList
- changed & to && when testing for a file because file.exist gives an error if a granges object is given

- vignette
- now looks ok, but more work could be done
- I spent a shitload of time to put the \wrapfigure at the top of the page, but was unable. Apparently wrapfigure breaks when put after a sectionbreak - if you manage to do this, I buy you a big beer
- corrected a typo

- readAnnotate.R:
- added examples

binMatrix:
- sorted it out for the GRangesList