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DEprot

Package to impute, normalize and perform differential analyses on proteomics data (LFQ-based)

update

harmonize.batches(): added algorithm (ComBat/limma), ComBat.mode, and block; limma helps on sparse designs where ComBat hits a singular matrix
harmonize.batches(): drop uncorrectable proteins with a warning, error on an empty result, and fix the algorithm/block defaults
load.counts2 automatically converts the counts into log2 transformed.
diff.analyses, diff.analyses.limma and diff.analyses.prolfqua now return, for each group, the standard deviation (sd.<group>) and standard error of the mean (sem.<group>) of the log2 expression values, plus lfcSE, the standard error of the log2(FoldChange). The new columns are appended at the end of the results table. lfcSE is NA when stat.test = "wilcoxon"
updated manual and vignette accordingly to take into account for these exceptions and modifications

Bug fixed in the PCA calculation, functions/objects concerned: perform.PCA, diff.analyses*, plot.PC.buplot and the test.toolbox, as well as the vignette and manual.

Added the function plot.PC.biplot.
Added the function SAINTq and the rime.dpo and rime.saintq datasets.
Updated plot.PC.scatter to allow for the separate plotting of x and y zero-lines.
Updated the vignette to include the new functions.

The result from randomize.missing.values is now included in a separate slot. Also the a new boxplot.random and randomization.method slots for the randomized scores have been added.
In the DEprot.objects the slot imputation has been renamed into imputation.method. Many functions have been changed accordingly.
Due to the addition of new slots, multiple functions have been adapted.
In the differential result tables now degrees of freedom and test statistic columns have been added.
For power calculation analyses, an estimation of the distribution of the statistics has been added in the results list. For this also the dependencies of the package have been updated.
For GSEA, gene ranking can be based now also on the test statistic value. Accordingly, the compare.ranking function have been updated to compare all three methods.
Update of the vignette to include the compare.imp.methods function and the new updates.
Fixing a bug in handling single-sample groups for randomize.missing.values function.

Bug fixing on the check.normality function, which was inverting the evaluation of the AD’s test p-value.
Update of the vignette
Update of the CITATION files

First release.