NEWS

anota2seq 1.9.1

Fixed coding that would results in errors in R version 4.0 related to used of class(...) == "x".

We added a new option to the output parameter of the anota2seqGetOutput function, more details can be found in the function help.
The quality control section of the vignette has been expanded with more details, furthermore we added an example of quality control of poorly normalized data as reference.
We removed the apvSlope and apvSlopeP columns from the output of analysis for total mRNA and translated mRNA as these values are not generated for RNA source differential expression analysis.

fixed a bug where in anota2seqPlotPvalues and anota2seqPlotFC the contrast names were not displayed correctly when selecting only 1 contrast in case there were multiple
Using the anota2seqRun function with custom filtering parameters for maxP was still based on a maxPAdj of 0.15. This has been fixed, i.e. when maxP filtering is applied no maxPAdj filter will be used.

We changes semantics buffering down into buffered (mRNA up) and buffering up into buffered (mRNA down) - so the interpretation is more intuitive.
Add customization options to anota2seqPlotFC and anotat2seqPlotPvalues functions
Fixed a bug where an unitialized object "regModes" was being accessed causing an uninformative error message.

renaming to adhere to Bioconductor naming style for classes, functions and data objects
correct mistake in man page of anota2seq_data
modify default values (no NULL default value for mandatory arguments)
fix a bug with argument fileName in the plot functions

the latex2 function of BiocStyle is now deprecated in the devel version of the package. Replace it by latex()
remove inst/doc and build/ folders
update man pages
change default value of assayNum in anota2seqDataSetFromSE to 1
formatting of anota2seq show method (and minor text edits in the description of the object)
fixed issues related to sortBy parameter in anota2seqSelSigGenes
minor text edits in messages given to user
fixed bug regarding threshold lines in anota2seqPlotFC
fixed bug in anota2seqSelSigGenes when useRVM = FALSE and only one gene is to be selected