allow data.frame argument for .read.msgfp.tsv
Merge branch 'master' of /slow/bioinfo/vcs/git/fbreitwieser/isobar-Rlib
set decode.titles to FALSE by default (slows down read.idfile)
add 'is.decoy' to identification columns
doc improvements
set default significance levels to 0.05
as.data.frame.IBSpectra: export realpeptide as peptide when available
convert I/L peptides only when necessary
Merge branch 'master' of dev1:/slow/bioinfo/vcs/git/fbreitwieser/isobar-Rlib
Merge branch 'master' of /slow/bioinfo/vcs/git/fbreitwieser/isobar-Rlib
fixed real peptide names
convert tapply result into vector to retain data.frame integrity
renamed funtion calcTwoSidedNormalProb to calcProbXDiffNormals and added argument 'alternative'
don't set attributes of allowed values in properties.r - caused problems with reloading the package with devtools package
added function calc.pep.delta.score [uses data.frame without AC column]
.fix.il.peptide now by default just performs an I/L substitution
Merge branch 'hotfix/fix-il-peptide'

Conflicts:
	R/utils.R
modified calc.startpos to also calculate the 'real' peptide sequence
added function .unique.or.collapse
added min.q to define quantile range