scoreMatrix.R:
	- typo correction tmp -> rpm
before push
Merge branch 'development' of github.com:al2na/genomation into development
scoreMatrixList.R:
	- fixed typo in intersectScoreMatrix

test.bam,test.bam.bai, test.bedGraph, test.bw
	- test files for working with bam and Bigwig files

ScoreMatrixTest.R:
	- added tests for ScoreMatrix:GRanges, GRanges
test*:
	- data files for testing

scoreMatrix.R:
	- examples fro binMatrix

ScoreMatrixTests:
	- tests for binMatrix
NAMESPACE:
	- added orderScoreMatrixList

scoreMatrix.R
	- renamed order to orderScoreMatrixList
	- fixed some small bugs
	- added examples

scoreMatrixBin.R
	- added error when all width(target) < bin.num

scoreMatrixList.R
	- fixed all errors

*Test.R
	- still in development
ScoreMatrixTests.R:
	- done

ScoreMatrixBinTests.R
	- done
Test files are done
findFeatureComb.R:
	- fixed a bug when use.names=TRUE
removed the GenomationTests.R
Moved the test files to the test folder

randomizeFeature.R:
	- removed the messages from the function
getRandomEnrichment.R:
	- added examples
Added example gtf file.
NAMESPACE:
	- just sorted the exports by name

gffFunctions.R:
	- transferred to readData.R

readData.R
	- updated the gffToGRanges to work from files

Merge branch 'development' of github.com:al2na/genomation into development

Conflicts:
	NAMESPACE
	man/binMatrix-methods.Rd
DESCRIPTION:
	- removed gffFunctions.R

readData.R:
	- added gffToGRanges
readData.R:
	- had to write gffToGRanges again, is working now
DESCRIPTION:
	- merged

scoreMatrixList.R:
	- merged

NAMESPACE:
	- changed orderScoreMatrixList to orderBy

Merge branch 'development' of github.com:al2na/genomation into development

Conflicts:
	R/scoreMatrixList.R
	genomation.Rproj
	man/ScoreMatrixList-methods.Rd
	man/orderBy-methods.Rd
Merge pull request #38 from frenkiboy/development

Development