fix news file

inst/NEWS.Rd

@@ -0,0 +1,119 @@
+\name{MSstatsTMTnews}
+\title{MSstatsTMT News}
+\encoding{UTF-8}
+
+\section{Changes in version 2.6.1 (2023-02-26) }{\itemize{
+  \item Minor change: update PhilosophertoMSstatsTMTFormat function
+  normalization
+}}
+
+\section{Changes in version 2.4.1 (2022-09-12) }{\itemize{
+  \item Minor change: fix the bug of data table in performing local
+  normalization
+}}
+
+\section{Changes in version 2.2.7 (2022-02-18)}{\itemize{
+  \item Minor change: extend PhilosophertoMSstatsTMTFormat function to have multiple types of input
+}}
+
+\section{Changes in version 2.2.6 (2022-02-14)}{\itemize{
+  \item Major change: add PhilosophertoMSstatsTMTFormat function as converter for outputs from Philosopher
+}}
+
+\section{Changes in version 2.2.5 (2021-10-25)}{\itemize{
+  \item Minor change: add different point shape to dataProcessPlotsTMT as indicator of imputed values
+}}
+
+\section{Changes in version 2.2.3 (2021-10-06)}{\itemize{
+  \item Minor change: fix the bug when df.prior is infinite
+}}
+
+\section{Changes in version 2.2.0 (2021-09-21)}{\itemize{
+  \item Major change: extend groupComparisonTMT() function to cover repeated measures design
+  \item Allow flexible order of condition in dataProcessPlotsTMT.
+  \item Fix bug in Condition label in dataProcessPlotsTMT.
+  \item Improve MSstatsTestSingleProteinTMT() by directly reading lmerTest output. This may make statistics slightly different due to different numeric accuracy
+  \item fix bug when condition name contains 'group'
+  \item change the x-axis order in profile plot
+}}
+
+\section{Changes in version 2.0.1 (2021-06-14)}{\itemize{
+  \item update comments of PD converter function
+  \item fix bug in proteinSummarization() function when MBimpute = F}}
+
+\section{Changes in version 2.0.0 (2021-05-14)}{\itemize{
+  \item Refactor the pacakge to make it modulized
+  \item parameter rmPSM_withMissing_withinRun was retired
+  \item change converter function output from data.frame to MSstatsValidated
+  \item change proteinSummarization() function output from data.frame to a list with two data.frames: FeatureLevelData and ProteinLevelData
+  \item change dataProcessPlotsTMT() function input from two data.frames to a list with two data.frames, which is the output of function proteinSummarization()
+  \item change groupComparisonTMT() function input from a data.frame to a list with two data.frames, which is the output of function proteinSummarization()
+  \item change groupComparisonTMT() function output from data.frame to a list with three items, ComparisonResult, FittedModel and ModelQC
+}}
+
+\section{Changes in version 1.8.2 (2020-12-17)}{\itemize{
+  \item Update progress bar
+  \item Update groupComparisonTMT to avoid reusing the local function copied from lmer pacakge}}
+
+\section{Changes in version 1.8.1 (2020-12-10)}{\itemize{
+  \item Add citation of the MSstatsTMT paper
+  \item Fix the bug in groupComparisonTMT() due to the update of dependent pacakge
+  \item Fix the bug in MedianPolish summarization
+  \item proteinSummarization(): replace the zero values with NA before and after peptide normalization}}
+
+\section{Changes in version 1.6.6 (2020-10-13)}{\itemize{
+  \item Fix the bug in converters due to fractions with same mean, sum and max values
+  \item Fix the bug in converters due to summaryforMultipleRows
+  \item Fix the bug in OpemMS converter due to duplicated rows}}
+
+\section{Changes in version 1.6.3 (2020-06-05)}{\itemize{
+  \item Allow NA in the annotation file}}
+
+\section{Changes in version 1.6.2 (2020-06-02)}{\itemize{
+  \item Fix the bug in proteinSummarization() function and make sure the input to dataProcess is data.frame}}
+
+\section{Changes in version 1.6.1 (2020-05-10)}{\itemize{
+  \item Update groupComparisonTMT() to make predictions for every protein}}
+
+\section{Changes in version 1.4.7 (2020-04-24)}{\itemize{
+  \item Update the NEWS file}}
+
+\section{Changes in version 1.4.6 (2020-04-14)}{\itemize{
+  \item Fix bug in groupComparison() for unbalanced design
+  \item Use df approximation from lmerTest to perform group comparison}}
+
+\section{Changes in version 1.4.5 (2020-03-01)}{\itemize{
+  \item Add new function OpenMStoMSstatsTMTFormat()}}
+
+\section{Changes in version 1.4.4 (2020-02-01)}{\itemize{
+  \item Fix bug in PDtoMSstatsTMTFormat(): remove redundant rows when combining multiple fractions
+}}
+
+\section{Changes in version 1.4.3 (2019-12-28)}{\itemize{
+  \item Fix bug in groupComparisonTMT(): very few measurements case previously doesn't work
+}}
+\section{Changes in version 1.4.2 (2019-12-20)}{\itemize{
+\item Add the column 'issue' to the output of groupComparisonTMT()
+}}
+\section{Changes in version 1.4.1 (2019-10-31)}{\itemize{
+\item Fix the bug in the PDtoMSstatsTMTFormat() due to different PD version
+}}
+\section{Changes in version 1.2.7 (2019-08-22)}{\itemize{
+\item Update normalization options in proteinSummarization() function to 
+include global protein normalization and local peptide normalization with respect to reference channel
+\item Fix the bug in the contrast comparison of groupComparisonTMT() function.
+}}
+\section{Changes in version 1.2.2 (2019-06-03)}{\itemize{
+\item Update the linear modeling in groupComparisonTMT() function. Implement 5 linear models.
+\item Update the format of annotation file. If the channel has no sample, add 'Empty' under 
+condition and BioReplicate columns.
+}}
+\section{Changes in version 1.2.0 (2019-05-03)}{\itemize{
+\item Fix bugs in groupComparisonTMT() when using lm() function
+\item Update the format of annotation file to include fraction column
+\item Remove the 'fraction' option from coverter functions
+\item Update the linear modeling in groupComparisonTMT() function
+}}
+\section{Changes in version 1.0.0 (2018-09-21)}{\itemize{
+\item Submitted to Bioconductor
+}}