VERSION 1.29.3
------------------------
o Update maVolPlot man page
VERSION 1.29.2
------------------------
o Update to getContrasts man page example to account for changes in limma::topTable
VERSION 1.29.1
------------------------
o Update to getContrasts to account for changes in limma::topTable
o Update to maVolPlot to account fo changes in limma::topTable
VERSION 1.23.1
------------------------
o Add coefCV to NAMESPACE
o Modify pcaPlot to allow user to omit the labelling
o Switch from gridExtra to patchwork in vignette
VERSION 1.23.0
------------------------
o Version bump for Bioconductor 3.20, no changes to package
VERSION 1.21.1
------------------------
o Added function `coefVar.R` to calculate and plot coefficient of variance
between all samples in a sample group.

VERSION 1.13.2
------------------------
o Fixed guide = FALSE to guide = "none".

VERSION 1.13.1
------------------------
o Fixed bug in computeDiffStats.

VERSION 1.9.4
------------------------
o Added documentation for new data set.

VERSION 1.9.3
------------------------
o New Feature: Added the function IRSnorm, which performs normalisation of
intensities across multiple TMT runs using a common reference sample (Internal
Reference Scale).

VERSION 1.9.2
------------------------
o Bug Fix: Update getContrastResults test reference
o Fix bug in is_validScalingFunction - switch from `are_equal` to `identical`

VERSION 1.9.1
------------------------
o Fix bug in getContrastRestults where file was written to `.txt`, file name 
  should now be correctly formed from the contrast name
VERSION 1.15.3
------------------------
o Fix for error in devtools::check tests caused by differing locales

VERSION 1.7.1
------------------------
o Change Vignette to HTML
o Add textsize argument to corrPlot
o Allow missing values in scaling normalisations

VERSION 1.3.2
------------------------
o Added mergePeptides to NAMESPACE
VERSION 1.3.1
------------------------
o Added mergePeptides function to summarize identical peptides to single peptide for specific protein.

VERSION 1.1.2
------------------------
Updates to vignette to avoid build errors when attempting to connect to Uniprot

VERSION 1.1.1
------------------------
 o Fixed bug in maVolPlot - github Issue 12:
    Previously the 'selectedGenes' argument used GeneSymbols to match genes to
highlight in the plot. Not all accessions are annotated with a GeneSymbol, and 
some GeneSymbols are linked to more than one Accession. This could lead to 
situations where incorrect genes were being highlighted due to duplicate 
entries or NAs. The function now accepts and matches to accessions instead - 
this is now noted in the man pages.
 o Fixed bug in convertToMSnset - github Issue 11:
    The function previously threw and error if the metadata was a tibble as it
needs to set row names. The function now tranforms the metadata object to a
data frame.

VERSION 1.1.0
------------------------
 o First Bioconductor Devel (Bioconductor 3.9)

VERSION 1.0.0
------------------------
 o First Bioconductor Release (Bioconductor 3.8)

VERSION 0.99.0
------------------------
 o initial version with the following functions implemented:

   + convertToMSnset
   + summarizeIntensities
   + normalizeQuantiles
   + normalizeScaling
   + groupScaling
   + rowScaling
   + regressIntensity
   + computeDiffStats
   + getContrastResults
   + assignColours
   + intensityPlot
   + intensityBoxplot
   + peptideIntensityPlot
   + pcaPlot
   + maVolPlot
   + corrPlot
   + rliPlot
   + hierarchicalPlot
   + plotMeanVar
   + coveragePlot

  

