NEWS

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MultiRNAflow 1.11.1

• R functions
  • Updated 13 R functions by adding the required indentation after #' in multi-line @importFrom directives to avoid the warning: @importFrom must use a hanging indent to span multiple lines. This warning was triggered when running devtools::document(). The 13 updated R functions are : DATAnormalization.R, DATAplotBoxplotSamples.R, DATAplotExpression1Gene.R, DEanalysisTime.R, DEplotAlluvial.R, DEplotBarplot.R, DEplotBarplotFacetGrid.R, DEplotBarplotTime.R, DEplotVolcanoMA.R, GSEAQuickAnalysis.R, HCPCanalysis.R, MFUZZanalysis.R, MFUZZclustersNumber.R.
• tests/testthat
  • Updated test-DEanalysisGroup.R to use withCallingHandlers() to suppress deprecation warnings generated by the UpSetR R package. These warnings are related to deprecated ggplot2 functions used internally by UpSetR and are not caused by the MultiRNAflow code.

MultiRNAflow 1.7.2

• Vignette (MultiRNAflow_vignette-knitr.Rnw)
  • We use now use.unsrturl=TRUE

MultiRNAflow 1.7.1

• R functions of the packages
  • myYlabelNorm() (included in the R function DATAplotExpressionGenes()): there were an error when the RPKM normalization were used.
  • GSEAQuickAnalysis():
    • replace size aesthetic by linewidth because : Using size aesthetic for lines was deprecated in ggplot2 3.4.0.
    • correction errors: print(gManhattan) to print(gproList$gManhattan)
  • MFUZZclustersNumber(): slight modification for correcting one warning "Removed 1 row containing missing values or values outside the scale range (geom_point())."
  • DEplotBarplot(): in the section "Examples", we replace c("Spe.Pos", "Spe.Neg", "Other") by c("UpRegulated", "DownRegulated", "Other").
  • DEplotBarplotFacetGrid(): in the section "Examples", we add Melt.Dat.2 <- stats::aggregate(Nb.Spe.DE~., data=Melt.Dat.2, sum) so Melt.Dat.2 is more representative of the data used by our function. We also modify the function to prevent recent warnings from ggplot2 (.data[["<col_names>"]]).
• Vignette (MultiRNAflow_vignette-knitr.Rnw)
  • We add our publication from Bioinformatics
  • we correct new errors produced by latex output
    • problem with the input max.level of the function str()
    • we correct the following new error 'Illegal parameter number in definition of \NewValue'
    • we use '\printbibliography' and '\addbibresource' in the preamble for the 'cleaner' biblatex interface.

MultiRNAflow 0.99.10

• Dependency packages:
  • we remove unnecessary dependencies: ggsci, methods, plyr, RcolorBrew, rlang, scales
  • we add the R package ggplotify from CRAN
• The package now contains 321 tests and the coverage is now 90%
• R functions of the packages
  • DEanalysisTimeAndGroup(): Correction when there are two time points by adding data.frame(X) as input of the function apply().
  • DATAplotExpression1Gene(): When data depends only on biological conditions, violin plots are plotted only if the number of individual per condition is >50.
  • For all the main functions, all results (plots too now) are now saved in the SummaryExperiment class object and can be accessed with the R function metadata (S4Vectors package).
  • PCAgraphics(): the 2D PCA graph with temporal links is now realized with ggplot2 and all 3D PCA graph is saved as ggplot2 object with the R package ggplotify
  • MFUZZclustersNumber(): the plot is now realized with ggplot2
  • PCAgraphics(), PCAanalysis() and HCPCanalysis(): the input D3.mouvment is now called motion3D
  • Many functions have been split into several parts to make the code easier to read
• Vignette (Running_analysis_with_MultiRNAflow.Rmd)
  • modification because of outputs and inputs modification
• Vignette (MultiRNAflow_vignette-knitr.Rnw)
  • modification because of outputs and inputs modification
  • update of the vignette in order to answer comment of reviewers of Bioinformatics

MultiRNAflow 0.99.9

Suggestions and remarks from a bioconductor team member

• modification of outputs in order to replace list ouputs by SE class object
• Vignette (Running_analysis_with_MultiRNAflow.Rmd)
  • modification because of ouputs modification
• More unit tests (now 197 unit tests in 31 files), coverage = 60/100

MultiRNAflow 0.99.8

Suggestions and remarks from a bioconductor team member

• Correction of DESCRIPTION file
• add a new function to improve inputs in others function
• modification of R functions depending on previous inputs
• Vignette (Running_analysis_with_MultiRNAflow.Rmd)
  • code-style to highlight (function, variable, package names)
  • keeping includegraphics only for the introduction part
• More unit tests (now 45 unit tests in 25 files)
• add the R file MultiRNAflow-package.R for man folder

MultiRNAflow 0.99.7

Suggestions and remarks from a bioconductor team member

• Correction of DESCRIPTION file
• Vignette (Running_analysis_with_MultiRNAflow.Rmd)
  • code-style to highlight (function, variable, package names)
  • More details about the vignette
  • eval=FALSE replaced by eval=TRUE
• More unit tests

MultiRNAflow 0.99.6

Bug fixes

• Necessary correction by the automated single package builder of bioconductor.org.

MultiRNAflow 0.99.0

• Added a NEWS.md file to track changes to the package.