CHANGES IN VERSION 1.2.3
-------------------------
BUG FIXES

 o Add fail-safe functionality to sample_annotation function for non-unique file names.


CHANGES IN VERSION 1.2.0
-------------------------
NEW FEATURES

 o SWATH2stats in BioC 3.3 release


CHANGES IN Version 1.1.17
-------------------------
DOCUMENTATION

 o updated NEWS file


CHANGES IN Version 1.1.16
-------------------------
BUG FIXES

 o Error fix in test_convert.R


CHANGES IN Version 1.1.15
-------------------------
DOCUMENTATION

 o Add Citation of PLoS ONE publication of SWATH2stats


CHANGES IN VERSION 1.1.14
-------------------------
DOCUMENTATION

 o import_data: minor changes in documentation
 o defining several functions at the beginning of function script


CHANGES IN VERSION 1.1.13
-------------------------
DOCUMENTATION

 o assess_fdr_byrun, assess_fdr_overall, filter_mscore_fdr: add sentence to manual page about FFT
 o vignettes: Add/change title
 
BUG FIXES

 o DESCRIPTION: add knitr to Suggests and VignetteBuilder, add R>=2.10.0 to Depends 


CHANGES IN VERSION 1.1.12
-------------------------
NEW FEATURES

 o sample_annotation: remove option column.runid.
 o assess_fdr_byrun and assess_fdr_overall: add option to set range of plotting with n.range

DOCUMENTATION

 o SWATH2stats_example_script, Spyogenes data: added Example script and S.pyogenes data


CHANGES IN VERSION 1.1.11
-------------------------
NEW FEATURES

 o plot_correlation_between_samples: import cor function from stats package and reorder y axis.


CHANGES IN VERSION 1.1.10
-------------------------
BUG FIXES

 o test for FDR filtering: bug fix due to fix in mscore4assayfdr


CHANGES IN VERSION 1.1.9
-------------------------
DOCUMENTATION

 o Update vignette

DEPRECATED AND DEFUNCT

 o remove function: filter_all_peptides

BUG FIXES

 o mscore4assayfdr: bug fix


CHANGES IN VERSION 1.1.8
-------------------------
BUG FIXES

 o add functions that were not updated


CHANGES IN VERSION 1.1.7
-------------------------
NEW FEATURES

 o added functions: count_analytes, plot_correlation_between_samples, plot_variation, plot_variation_vs_total, transform_MSstats_OpenSWATH.
 o filter_mscore_requant renamed to filter_mscore_freqobs


BUG FIXES

 o sample_annotation: Bug fix - it reported upon error different conditions instead of filenames.
 o assess_fdr_overall: Correction of transition level column name from "id" to "transition_group_id"
 o assess_fdr_byrun: Correction of transition level column name from "id" to "transition_group_id"
 o plot.fdr_cube: added na.rm=TRUE to plotting functions


CHANGES IN VERSION 1.1.6
-------------------------
BUG FIXES

 o Correction of typographical error in Vignette for Wolski et al.


CHANGES IN VERSION 1.1.5
-------------------------
BUG FIXES

 o Bug fixes for assess_fdr_byrun that was also introduced into version v1.0.2 at the same time. It fixes problems with labelling the runs correctly in some cases.


CHANGES IN VERSION 1.1.4
-------------------------
BUG FIXES

 o Bug fixes in test_convert.


CHANGES IN VERSION 1.1.1
-------------------------
NEW FEATURES

 o Improved the function disaggregate() that also data with different number of transitions per precursor than 6 can be used
 o Added tests for disaggregate.R and convert4pythonscript.R


CHANGES IN VERSION 1.1.0
-------------------------
NEW FEATURES

 o Development version of SWATH2stats in BioC 3.3


CHANGES IN VERSION 1.0.0
-------------------------
NEW FEATURES

 o SWATH2stats in BioC 3.2 release


CHANGES IN VERSION 0.99.5
-------------------------
NEW FEATURES

 o SWATH2stats package accepted to Bioconductor