Merge pull request #18 from frenkiboy/development

Development
Merge pull request #22 from frenkiboy/development

Development
Merge pull request #23 from frenkiboy/development

Development
changes to vignette (still working on it), removed data from extdata.
 changes to inline comments, build&reload works with one warning I can't figure out
updated gitignore
readData methods contains a new version of readGeneric(), all functions there now S3. namespace and rd files are updated.
comment added to readData.R
scoreMatrix->ScoreMatrix
in ScoreMatrix, "weight.col" argument is replaces "col.name"
scoreMatrix -> ScoreMatrix and ScoreMatrixBin for all
a comma is removed
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)