Changed cat -> message in all files.
scoreMatrixList.R
	- added the functionality to work with multiple bam files

scoreMatrix.R
	- can't figure out what I changed :|
scoreMatrixList.R:
	- added the order function
scoreMatrix.R:
	- started fixing heatMatrix
Merge branch 'development' of github.com:al2na/genomation into development

Conflicts:
	R/scoreMatrixList.R
scoreMatrixList.R:
	- added the functionality to make ScoreMatrixList from genomic
	  ranges

rooxygenize2 and install passed, but deleted the Rd files
readData.R:
	- just removed some whitespace

scoreMatrix.R:
	- changed the heatMatrix so that the factor plotting is optional
	- does not plot the factor names - I have absolutely no idea why
GenomationManual-knitr.Rnw
	- sorted out a typo

.gitignore
	- added GenomationDevtools.R
scoreMatrix.R:
	- added the functionality to provide a param object when working
	  with bam files directly
scoreMatrix.R:
	- sorted some whitespace

GenomationManual-knitr.Rnw
	- writing chipseq binding
readData.R:
	- replaced str_detect/str_replace with grepl and sub
scoreMatrix.R
	- added the functionality to provide custom param parameters for
	  custom filtering of bed files
	- added unique and extend paramters, so that the user can control
	  what kind of reads to use

scoreMatrixBin.R
	- added the functionality to work directly with bam files

DESCRIPTION
	- added Rsamtools as dependency

NAMESPACE
	- added import(Rsamtools)
scoreMatrixList.R
	- added a for loop to the sml constructor

scoreMatrisBin.R
	- added reading from files

scoreMatrix.R
scoreMatrixBin.R, scoreMatrixList.R:
	- added the bin.op argument - I do not understand why the function
	  does not call the default value in the generic
scoreMatrixList.R:
	- added automatic name generating to sml
findFeatureCombination.R:
	- removed the if clause if only one range is present

scoreMatrix.R:
	- changed the scale function in the scaleScoreMatrix to
	  (x-mean(x))/(max(x)-min(x)+1)

scoreMatrixList.R:
	- scaleScoreMatrixList:
		- removed the default value for scale

GenomationManual-knitr.Rnw
	- 2 subsections finished
DESCRIPTION:
	- added ggplot2 import
DESCRIPTION, NAMESPACE:
	- added ggplot2 to import
DESCRIPTION:
	- removed methods from namespace dependencies
Did Rcmd check - still get four errors about documentation
plotMatrix.R:
	- file for matrix visualization functions

scoreMatrix.R, scoreMatrixList.R:
	- moved heatMatrix and heatmapProfile to plotMatrix.R

DESCRIPTION:
	-added plotMatrix file for export

TabFiles:
	- data folder for holding various table files for showing
	  readGeneric possibilities
	- will use the hg19 cpg islands with permutted columns