Merge pull request #7 from frenkiboy/development

Development
Merge pull request #8 from frenkiboy/development

Corrected the function names in the NAMESPACE file
delete unused data from Data folder
NAMESPACE corrected| changed function names were not propagated correctly, that is changed now
version bump
First commit of the genomation manual file.
new data added, and the script that generates the data is in the scripts directory
Commit before al2na pull.
Merge branch 'development' of github.com:al2na/genomation into development
DESCRIPTION: added knitr as vignette builder
Started the chapters on the vignette.
dataAnalysis.pdf: pipeline from the Comgenr book, the annotation data is
highlighted - still not certain how to load the pdf using relative paths.
GenomationManula.Rnw: vignette update
Developing exercises for the genomationManual.
findTFComb.R - a function that finds the combinatorics of tf binding.
findTFComb.R: finished and working
readAnnotate.R: corrected a bug in .readTableFast - was reading characters
as factors
readData.R: file for function for reading data
Moved .readTableFast and readBed from readAnnotate.R to readData.R

Moved .readTableFast and readBed from readAnnotate.R to readData.R
renamed the location paramater form readBed to file - I think file should
be used as a standard parameter to designate file paths.
findTfComb.R: corrected the return value in the documentation
readData.R: rewritten the readBam function to be more flexible - it uses
now the GRanges function for conversion between data frames and granges
DESCRIPTION: added readTfComb.R and readData.R to collate
NAMESPACE: added readTFComb, readBroadPeak and readNarrowPeak to export
version bump to 0.4.2