* mcq.compute.anova.contrast : function to compute anova using contrast description adapted from Lambert I., Paysant-Le Roux C., Colella S., Martin-Magniette M.-L. (2020) DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models. Plant Methods, 16:68 see ?mcQ.Compute.anova.contrast for details
* mcq.compute.anova.contrast : function to compute anova using contrast description adapted from Lambert I., Paysant-Le Roux C., Colella S., Martin-Magniette M.-L. (2020) DiCoExpress: a tool to process multifactorial RNAseq experiments from quality controls to co-expression analysis through differential analysis based on contrasts inside GLM models. Plant Methods, 16:68 see mcq.compute.anova.contrast. See help for details
* mcq.select.pvalues.contrast : function to select proteins matching criteria in cmcq.anova.contrast object. See help for details
* mcq.print.contrast.names : function to prin contrast names to facilitate the selection with mcq.select.pvalues.contrast. See help for details
* mcq.select.from.peptlist : function to manipulate peptide list for relevant object. See help for details
## Modification
* mcq.plot.intensity.violin : invsion of the two graph in case of normalized data to be consistent with mcq.plot.intensity.profile
* mcq.plot.intensity.violin : division of the two graph in case of normalized data to be consistent with mcq.plot.intensity.profile
* mcq.read.diann : adding to option nSeqPerProt allow to select the minimal number of different sequence required to consider a proteine and inference only one option for the moment specific that select only Protein.Group with one accession.
* mcq.compute.anova : adding a trycatch duirng computation of model with clean error message for protein without variation
* mcq.compute.anova : modification of argument name inter to interaction to be consistent with newly mcq.compute.anova.contrast function
* mcq.get : correction of a bug with cmcq.ratio object
* mcq.plot.tukey : suppression of argument qprot data were now take form cmcq.anova object and stocked in cmcq.tukey object
* mcq.plot.tukey : suppression of argument qprot. Data were now take form cmcq.anova object and stocked in cmcq.tukey object
* mcq.plot.violin : correction of a bug that produce empty plot
* mcq.compute.anova : now can work with peptide level and labelling object at peptide level
* mcq.select.pvalues : retturn a cmcq.protlisst or cmcq.peplist dependanding one which type of objecct was used in mcq.ccompute.anova
## Removed function
* mcq.get.compar : replace by mcq.get. Use wide format to have an compar table see mcq.get function for details
* mcq.get.dataframe : replace by mcq.get. Use long format to have an compar table see mcq.get function for details
* mcq.get.compar : replace by mcq.get. Use wide format to have an compar table. See mcq.get function help for details
* mcq.get.dataframe : replace by mcq.get. Use long format to have an compar table. See mcq.get function help for details
* mcq.write.compare : replace by mcq.write design to work with output of mcq.get function . See mcq.write function help for details
* mcq.write.dataframe : replace by mcq.write design to work with output of mcq.get function . See mcq.write function help for details
* mcq.write.merge : replace by mcq.write design to work with output of mcq.get function . See mcq.write function help for details
thierry <thierry.balliau@inrae.fr>