NEWS

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qPLEXanalyzer 1.29.3

• Update maVolPlot man page

qPLEXanalyzer 1.29.2

• Update to getContrasts man page example to account for changes in limma::topTable

qPLEXanalyzer 1.29.1

• Update to getContrasts to account for changes in limma::topTable
• Update to maVolPlot to account fo changes in limma::topTable

qPLEXanalyzer 1.23.1

• Add coefCV to NAMESPACE
• Modify pcaPlot to allow user to omit the labelling
• Switch from gridExtra to patchwork in vignette

qPLEXanalyzer 1.23.0

• Version bump for Bioconductor 3.20, no changes to package

qPLEXanalyzer 1.21.1

• Added function 'coefVar.R' to calculate and plot coefficient of variance between all samples in a sample group.

qPLEXanalyzer 1.15.3

• Fix for error in devtools::check tests caused by differing locales

qPLEXanalyzer 1.13.2

• Fixed guide = FALSE to guide = "none".

qPLEXanalyzer 1.13.1

• Fixed bug in computeDiffStats.

qPLEXanalyzer 1.9.4

• Added documentation for new data set.

qPLEXanalyzer 1.9.3

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

qPLEXanalyzer 1.9.2

• Bug Fix: Update getContrastResults test reference
• Fix bug in is_validScalingFunction - switch from 'are_equal' to 'identical'

qPLEXanalyzer 1.9.1

• Fix bug in getContrastRestults where file was written to '.txt', file name should now be correctly formed from the contrast name

qPLEXanalyzer 1.7.1

• Change Vignette to HTML
• Add textsize argument to corrPlot
• Allow missing values in scaling normalisations

qPLEXanalyzer 1.3.2

• Added mergePeptides to NAMESPACE

qPLEXanalyzer 1.3.1

• Added mergePeptides function to summarize identical peptides to single peptide for specific protein.

qPLEXanalyzer 1.1.2

Updates to vignette to avoid build errors when attempting to connect to Uniprot

qPLEXanalyzer 1.1.1

• 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.
• 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.

qPLEXanalyzer 1.1.0

• First Bioconductor Devel (Bioconductor 3.9)

qPLEXanalyzer 1.0.0

• First Bioconductor Release (Bioconductor 3.8)

qPLEXanalyzer 0.99.0

• 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