## ----style, echo = FALSE, results = 'asis'------------------------------- BiocStyle::markdown() ## ----global_options, include=FALSE-------------------------------------------------------------------------- knitr::opts_chunk$set(fig.width=10, fig.height=7, warning=FALSE, message=FALSE) options(width=110) ## ----------------------------------------------------------------------------------------------------------- ## load package require(MSstatsBioData) ## require SRM_yeast data data(SRM_yeast) ## look at first lines head(SRM_yeast) ## ----------------------------------------------------------------------------------------------------------- ## Example of using MSstats for differential abundance analysis. require(MSstats) input.proposed <- dataProcess(SRM_yeast, summaryMethod="TMP", cutoffCensored="minFeature", censoredInt="0", MBimpute=TRUE, maxQuantileforCensored=0.999) ## ----------------------------------------------------------------------------------------------------------- ## set up the comparison that you want. comparison1<-matrix(c(-1,1,0,0,0,0,0,0,0,0),nrow=1) comparison2<-matrix(c(-1,0,1,0,0,0,0,0,0,0),nrow=1) comparison3<-matrix(c(-1,0,0,1,0,0,0,0,0,0),nrow=1) comparison4<-matrix(c(-1,0,0,0,1,0,0,0,0,0),nrow=1) comparison5<-matrix(c(-1,0,0,0,0,1,0,0,0,0),nrow=1) comparison6<-matrix(c(-1,0,0,0,0,0,1,0,0,0),nrow=1) comparison7<-matrix(c(-1,0,0,0,0,0,0,1,0,0),nrow=1) comparison8<-matrix(c(-1,0,0,0,0,0,0,0,1,0),nrow=1) comparison9<-matrix(c(-1,0,0,0,0,0,0,0,0,1),nrow=1) comparison <- rbind(comparison1,comparison2,comparison3, comparison4,comparison5,comparison6, comparison7,comparison8,comparison9) row.names(comparison) <- c("T2-T1","T3-T1","T4-T1", "T5-T1","T6-T1","T7-T1", "T8-T1","T9-T1","T10-T1") ## ----------------------------------------------------------------------------------------------------------- ## test between comparison you set up. output.comparison <- groupComparison(contrast.matrix=comparison, data=input.proposed) ## output.comparison$ComparisonResult include the result of testing. head(output.comparison$ComparisonResult)