Minor change: update PhilosophertoMSstatsTMTFormat function normalization
Minor change: fix the bug of data table in performing local normalization
Minor change: extend PhilosophertoMSstatsTMTFormat function to have multiple types of input
Major change: add PhilosophertoMSstatsTMTFormat function as converter for outputs from Philosopher
Minor change: add different point shape to dataProcessPlotsTMT as indicator of imputed values
Minor change: fix the bug when df.prior is infinite
Major change: extend groupComparisonTMT() function to cover repeated measures design
Allow flexible order of condition in dataProcessPlotsTMT.
Fix bug in Condition label in dataProcessPlotsTMT.
Improve MSstatsTestSingleProteinTMT() by directly reading lmerTest output. This may make statistics slightly different due to different numeric accuracy
fix bug when condition name contains 'group'
change the x-axis order in profile plot
update comments of PD converter function
fix bug in proteinSummarization() function when MBimpute = F
Refactor the pacakge to make it modulized
parameter rmPSM_withMissing_withinRun was retired
change converter function output from data.frame to MSstatsValidated
change proteinSummarization() function output from data.frame to a list with two data.frames: FeatureLevelData and ProteinLevelData
change dataProcessPlotsTMT() function input from two data.frames to a list with two data.frames, which is the output of function proteinSummarization()
change groupComparisonTMT() function input from a data.frame to a list with two data.frames, which is the output of function proteinSummarization()
change groupComparisonTMT() function output from data.frame to a list with three items, ComparisonResult, FittedModel and ModelQC
Update progress bar
Update groupComparisonTMT to avoid reusing the local function copied from lmer pacakge
Add citation of the MSstatsTMT paper
Fix the bug in groupComparisonTMT() due to the update of dependent pacakge
Fix the bug in MedianPolish summarization
proteinSummarization(): replace the zero values with NA before and after peptide normalization
Fix the bug in converters due to fractions with same mean, sum and max values
Fix the bug in converters due to summaryforMultipleRows
Fix the bug in OpemMS converter due to duplicated rows
Allow NA in the annotation file
Fix the bug in proteinSummarization() function and make sure the input to dataProcess is data.frame
Update groupComparisonTMT() to make predictions for every protein
Update the NEWS file
Fix bug in groupComparison() for unbalanced design
Use df approximation from lmerTest to perform group comparison
Add new function OpenMStoMSstatsTMTFormat()
Fix bug in PDtoMSstatsTMTFormat(): remove redundant rows when combining multiple fractions
Fix bug in groupComparisonTMT(): very few measurements case previously doesn't work
Add the column 'issue' to the output of groupComparisonTMT()
Fix the bug in the PDtoMSstatsTMTFormat() due to different PD version
Update normalization options in proteinSummarization() function to include global protein normalization and local peptide normalization with respect to reference channel
Fix the bug in the contrast comparison of groupComparisonTMT() function.
Update the linear modeling in groupComparisonTMT() function. Implement 5 linear models.
Update the format of annotation file. If the channel has no sample, add 'Empty' under condition and BioReplicate columns.
Fix bugs in groupComparisonTMT() when using lm() function
Update the format of annotation file to include fraction column
Remove the 'fraction' option from coverter functions
Update the linear modeling in groupComparisonTMT() function
Submitted to Bioconductor