NEWS: TPP

Version 1.0.0:
  
  o First release of the TPP package for analyzing Thermal Proteome Profiling 
    experiments.

Version 1.1.0:
  o Changes in devel will be characterized by version number 1.1.x

Version 1.1.1:

  o bugfixes in config table import from .csv files: 
    1. can now handle different types of delimitors (";", "\t", ",")
    2. automatically removes empty rows after import

Version 1.1.2:
  o the recent update of the gridExtra package to Version 2.0.0 required a small fix to 
    ensure sucessful plotting of the melting curves and parameter tables, as well as correct
    display of QC 'bottleplots'.

Version 1.1.3:
  o fixed problem in QC-plot generation due to the gridExtra package update: 
    adapted height parameter in grid.arrange

Version 1.1.4:
  o Curve parameters "a" and "b" are now reported in the output of analyzeTPPTR and tpptrCurveFit.

Version 1.2.5:
  o CCR-part: 
      fold changes can now be normalized to their lowest temperature during 
      import by the function tppccrNormalizeToReference. 
      This ensures that the transformed values will always be between 0 and 1.
      When normalizing to the lowest concentration, and this value is 0, a small 
      constant (1e-15) is added to prevent division by zero.
  o CCR-import:
      Argument nonZeroCols can be NULL if no additional filtering is needed.
  o CCR output: 
      To make filtering easier, the 'passed_filter' column now shows 
      FALSE even if proteins could not be used for fitting (instead of NAs).
  o CCR output: 
      To make filtering easier, the 'passed_filter' column now shows 
      FALSE even if proteins could not be used for fitting (instead of NAs).
  o CCR output: 
      column with normalization results was renamed from 'normalized' 
      to 'median_normalized' to distinguish from the newly introduced normalization 
      to value at lowest concentration.
  o Excel export: 
      Columns are only color-coded by experiment, when the number of
      experiments is > 1.
  o Excel export: 
      Columns are only color-coded by experiment when the number of
      experiments is > 1.
  o Excel export:
      Relative paths to the plots work now for TR- and CCR part
  o Bug fix for data import: 
      Unique identifiers now treated correctly again.
  o Bug fix for Excel output: 
      Boolean column entries are only transformed to  "yes"/"no" for non-missing values.
  o Bugfix in TR-QC plots: 
      do not attempt to create Tm difference histograms if only one experiment is provided.
  o Bugfix in TR normalization: 
      fixedReference argument works again
  o Bugfix in TR-QC plots: 
      do not attempt to plot minSlope vs. Tm-diffs if no valid Tm-diff values are available.

Version 2.1.0:
  o Major update to the CCR-part: It is now possible to fit and plot multiple
    experiments simultaneously.
  o It is now possible to perform user-specified comparisons of different 
    experiments. They are specified in the 'comparison' column of the config 
    table.
  o TR-part: Hypothesis testing is now separated from result table creation. Therefore, 
    a new function was introduced (tpptrAnalyzeMeltCurves) -> see vignette.
  o CCR-part: Curve fitting and plotting are now conducted by separate functions -> see
    vignette.
  o Bug fixes
  o Introduced color coding of the columns belonging to different experiments in 
    the excel output. This requires openxlsx version >= 2.4.0.
  o The CCR workflow now only returns normalized measurements if normalization was 
    actually performed. Unmodified measurements are always returned and indicated 
    by the suffix 'unmodified'.
  o Data import from tab-delimited files now ignores quotes so that protein annotation 
    fields can contain single ' or " characters.
  o Now enabling arbitrary numbers of plot colors for melting curves or dose response 
    curves.

Version 2.1.1:
Updated package vignette.
  
2.1.2 (Nov-19-2015):
  o Bugfix in config table import:
      All non-alphanumeric characters in the Experiment column are now replaced 
      by'_'.
 o Bugfix in QC scatter plots:
      Can now handle cases where protein IDs do not overlap between experiments,
      or where the temperatures differ between experiments. The affected plots 
      are left empty and contain a message to explain the problem.
      
2.1.3 (Dec-17-2015):
 o Added column 'pEC50_quality_check' to CCR output to filter out pec50 values 
 not within concentration ranges.
 
2.1.4 (Dec-23-2015)
 o Removed example dataset containing fitted data from the Data folder in order 
   to reduce the overall package size (it was only used by some examples in the 
   function documentation). 
 o Minor changes to documentation in order to ensure that R CMD check and 
   BiocCheck run again without warnings.
   
2.1.5 (Jan-04-2015)
 o Now selectively importing functions from grid and gridExtra package to  
   prevent 'double import' warning due to recent changes in ggplot2.
   
2.1.6 (Jan-18-2016)
 o New CCR output column 'pEC50_quality_check' now reports pec50 values with
   the same sign as the 'pec50' column.
   

2.3.2 (Apr-16-2016)
Removed unit test that causes R CMD check to crash  since the latest update of package 'testthat'.

2.3.3 (Jun-02-2016)
Fixed bug in plotColors for the case when no comparisons are specified
   
2.99.0 (Oct-06-2016)
 o Major update: Extended package to analyze 2D-TPP experiments
 o Major update: Extended package to analyze TPP-TR experiments by 
   "non-parametric analysis of response curves" (NPARC), a non-parametrc 
    spline-based test for treatment effects.
 o Bugfix in 'tpptrCurveFit': restrict file names to 255 characters when creating
   melting curve plots in order to prevent file system crashes.
 o New packages dependencies: dplyr, margrittr
 o Bugfix in CCR workflow: avoid division by 0 when transforming foldchanges 
   before dose-response curve fitting.
   
2.99.1 (Oct-12-2016)
 o Remove the complex reference data object from the data folder. Will be re-
   introduced lalter in a leaner format.

2.99.2 (Oct-12-2016)
 o Reduce data by "xz" compression
   
2.99.3-5 (Oct-16-2016)
 o Adapt notation of function names and input arguments for consistency with 
   1D (TPP-TR and TPP-CCR) part.

3.0.0 (Oct-18-2016)
 o New Bioconductor release candidate!

Changes in version 3.1.3 (Dec-07-2016):
 o Bug fix: ensure correct handling of drug concentrations when they are imported in scientific notation (xx.xxE-x)

Changes in version 3.1.3 (Feb-05-2017):
 o Deprecate functions and arguments, primarily those used in the first version 
 of TPP-2D analysis workflow.
 o Bug fixes:
  - sort x and y values before DR curve fitting because the functions for initial parameter estimation are dependent on the correct ordering
  - supress useless VD logfiles when creating VENN diagrams

Changes in version 3.2.0 (Feb-13-2017):
 o Changes to the Excel output of TPP-TR experiments: 
 - Plot paths in excel output are stored in separate columns for spline and melting curve fits
 - Reported p-values for Tm based analysis are now increased in value after removing a bug in their calculation. The thresholds applied for determining significant hits have been updated justed accordingly.
 
 o Improvements to the 2D-TPP analysis:
  - Split rows with multiple identifiers (e.g. separated by '|') into separate rows  (was already present in TR- and CCR analysis)
  - Sort result table rows by temperature for each ID

Changes in version 3.2.2 (Mar-12-2017):
 o Bug fix in the TPP-TR analysis: 
 - It is now possible to leave the 'otherRequirements' slot empty in the object containing the normalization criteria. 

3.5.0 (May-01-2017)
 o New Bioconductor release candidate!

Changes in version 3.5.14 (May-02-2017):
 o Importing the whole tidyverse instead of ggplot2, dplyr etc. individually
 o Shift Biobase, dplyr and tidyr to "depends" so that they are automatically availabe for downstream analyses.
 o Add the option to use the 'old' config table with a Replicate column. On the support site, users expressed confusion that this column was deprecated since the Nature Protocols paper release. Now, the comparison columns are automatically generated from the replicate column, if only the replicate column is defined as described in the old documentation.

3.13.1 (Okt-08-2019)
 o Avoid warnings due to factor/character conversions in vignette 
 
3.13.2 (Okt-12-2019)
  o Revise vignette
  
3.13.3 (Okt-15-2019)
 o defunct the following functions: tpp2dPlotCCRGoodCurves, tpp2dPlotCCRAllCurves, 
   tpp2dPlotCCRSingleCurves, tpp2dEvalConfigTable, tpp2dRemoveZeroSias, 
   tpp2dReplaceColNames, tpp2dCreateCCRConfigFile
   
3.15.1 (Jan-31-2019)
 o remove dependency to the sme package because it is not available any more on CRAN.
 

3.17.0
 o New Bioconductor release candidate

3.17.1
 o Fixed bug in tpp2dCreateTPPTRreferenece upon user request (#10)
  o removed adding spline fit column from 2DTPP output table
  o fixed bug in tpp2dCreateTPPTRReference and made example in vignette work
  o removed leftover parameters in tpp2dCreateTPref function
  o final fix of tpp2dCreateTPPTRreference and call in vignette now works

3.17.2-3
 o Fixed bugs and warnings after update to dplyr v1.0.0.

3.17.4
  o fix errors in build report on Bioconductor
  o fix warnings due to conversion of non-numeric values during 2D-TPP import
  o fix warnings in ggplot command
  o upgrade deprecated dplyr functions
  o make syntax of testthat checks more consistent across files

3.17.5
 o fix bugs and warnings in executable examples
 
3.17.6
 o fix warnings due to unused argument of select(!!!syms(...)) statement during histogram generation for
reference data

3.27.1
 o Fixed bugs and warnings after dplyr update
 
3.39.1
 o Avoid deprecated dplyr::tbl_df() calls in biobroom::tidy.ExpressionSet() by changing output to data.frame for compatibility with dplyr ≥ 1.0.0.
 o Deprecated parallelization and nCores parameter in fitting and plotting functions to improve maintainability and robustness to dependency changes.
 o Fixed ggplot2 deprecation warning to maintain compatibility with recent ggplot2 versions