format lightgray when field value is FALSE
added option to use 'complete.obs' (like in standard cor) to remove NA values
create 'quant.tbl.notlocalized' only when the column 'pep.siteprobs' is present
bugfix for not-localized table
added option to show progress bar on calcProbXDiffNormals
correct naming of report files (might have been quant.NAME.pdf, etc ..)
better messages
add 'Channels' as column to XLS report, if appropriate
always show peptide modification context
as.concise.df: show real.peptide column only when needed
improved getPeptideModifContext to show context in real (ie not only L) sequence
various fixes for ratiosReshapeWide: include interger columns when reshaping
use plyr to get ac into empty result sets
Merge branch 'master' of /slow/bioinfo/vcs/git/fbreitwieser/isobar-Rlib

Conflicts:
	R/ratio-methods.R
	R/utils.R
added .getModifOnPosition which returns for a modifstring the modification at the defined position
minor fixes
added argument to load a protein group for the peptide ratio correction
Merge branch 'master' of dev1:/slow/bioinfo/vcs/git/fbreitwieser/isobar-Rlib

Conflicts:
	R/ratio-methods.R