First commit of the genomation manual file.
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
Merge branch 'development' of github.com:al2na/genomation into development
scoreMatrix.R: removed GetViews - it's obsolete
scoreMatrix seems legit now - have to run test though
Merge pull request #18 from frenkiboy/development

Development