exporting Grp2Analysis class

NAMESPACE

@@ -1,13 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Grp2Analysis)
 export(MQtoMSstatsFormat)
 export(SRMService)
 export(getIntensities)
 export(getRequiredColumns)
 export(piwotPiw)
 export(plotNicely)
+exportClasses(Grp2Analysis)
 exportClasses(SRMService)
 import(DBI)
 import(methods)
 import(parallel)
 import(quantable)
+import(reshape2)

R/Grp2Analysis.R

@@ -1,12 +1,10 @@
 annotationColumns <- c("Raw.file","Condition", "BioReplicate", "Run","IsotopeLabelType")
 proteinColumns <- c("ProteinName","TopProteinName","nrPeptides")
 
-#'
+#' Perform 2 group analysis with visualization
 #' @export Grp2Analysis
 #' @exportClass Grp2Analysis
 #'
-#' @examples
-#' Grp2Analysis()
 Grp2Analysis <- setRefClass("Grp2Analysis",
                             fields = list( proteinIntensity = "data.frame",
                                            annotation = "data.frame",

R/SRMService.R

@@ -195,13 +195,19 @@ SRMService <- setRefClass("SRMService",
                               )
                               return(int_)
                             },
+                            stripLabel=function(int_,light=FALSE){
+                              label<-if(light){.self$lightLabel}else{.self$heavyLabel}
+                              rownames(int_) <- gsub(paste("_",label,"$",sep=""),"",rownames(int_))
+                              invisible(int_)
+                            }
+                            ,
                             getMatchingIntensities = function(){
                               "get matrix with intensities, where nr of NAs in row < maxNA"
                               intLight_ <- .self$getTransitionIntensities(light=TRUE)
                               intHeavy_ <- .self$getTransitionIntensities()
 
-                              rownames(intLight_) <- gsub("_light$","",rownames(intLight_))
-                              rownames(intHeavy_) <- gsub("_heavy$","",rownames(intHeavy_))
+                              intLight_ <- stripLabel(intLight_, light=TRUE)
+                              intHeavy_ <- stripLabel(intHeavy_)
 
                               idx <-intersect(rownames(intLight_),rownames(intHeavy_))
 

inst/samples/grp2analysisTest.R

@@ -2,6 +2,7 @@ rm(list=ls())
 
 protein <- read.csv("d:/googledrive/DataAnalysis/p2084/215579/proteinGroups.txt",sep="\t",stringsAsFactors = F)
 
+colnames(protein)
 
 rawF <-gsub("Intensity\\.", "", grep("Intensity\\.",colnames(protein),value=T) )
 
@@ -13,24 +14,11 @@ annotation <-data.frame(Raw.file = rawF,
                         IsotopeLabelType = rep("L",length(condition)), stringsAsFactors = F)
 
 
+library(SRMService)
 
-source("R/Grp2Analysis.R")
-
-
-grp2 <- Grp2Analysis(annotation, "p2084BlaBla", maxNA=8  , nrPeptides=3)
-grp2$setHeatmap("red")
-
+grp2 <- Grp2Analysis(annotation, "p2084BlaBla", maxNA=8  , nrPeptides=2)
 grp2$setMQProteinGroups(protein)
 
-grp2$getDesignMatrix()
-
-
 library(dScipa)
-idx <-grep("SL9B2_MOUSE",rownames(grp2$proteinIntensity))
-grp2$proteinIntensity[idx,]
-res.eb <- grp2$getPValues()
-head(res.eb)
-grep("SL9B2_MOUSE",rownames(res.eb))
-
 rmarkdown::render("inst/reports/Grp2Analysis.Rmd",output_format = "pdf_document", output_file = "Grp2Analysis.pdf")