From c31a13f72a9545a30a1c6f2085f2435735efc85d Mon Sep 17 00:00:00 2001
From: Witold Wolski <wewolski@gmail.com>
Date: Mon, 6 Apr 2020 16:29:09 +0200
Subject: [PATCH 1/6] Update Run_MQ_QuantTwoGroupAnalysis.R

---
 inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R b/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R
index 34ed3b4..9dbf259 100644
--- a/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R
+++ b/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R
@@ -11,6 +11,7 @@ library(SRMService)
 ### Protein groups file
 packagedir <- path.package("SRMService")
 
+####! set the path to the proteinGroups.txt file.
 proteinGroupsFile <- file.path(packagedir, "samples/proteinGroups/proteinGroups.txt")
 
 ###
@@ -21,9 +22,14 @@ colnames(protein) <- make.names(colnames(protein))
 tmp <- cumsum(rev(table(protein$Peptides)))
 barplot(tmp[(length(tmp)-5):length(tmp)],ylim=c(0, length(protein$Peptides)),xlab='nr of proteins with at least # peptides')
 
-
+##
 rawF <- gsub("Intensity\\.", "", grep("Intensity\\.",colnames(protein),value=T) )
+
 condition <- quantable::split2table(rawF)[,3]
+
+# Raw.file <- c("23bb","23bcd","23ddd","","","")
+# condition <- c("baseline","baseline","w1","w1")
+
 annotation <- data.frame(Raw.file = rawF,
                          Condition = condition,
                          BioReplicate = paste("X",1:length(condition),sep=""),

From d15854d146e7587d0a6ac0a445d8288b54350360 Mon Sep 17 00:00:00 2001
From: Witold Wolski <wewolski@gmail.com>
Date: Tue, 28 Apr 2020 11:10:36 +0200
Subject: [PATCH 2/6] Update introduction-to-service.Rmd

---
 vignettes/introduction-to-service.Rmd | 1 -
 1 file changed, 1 deletion(-)

diff --git a/vignettes/introduction-to-service.Rmd b/vignettes/introduction-to-service.Rmd
index a5196e4..4d39397 100644
--- a/vignettes/introduction-to-service.Rmd
+++ b/vignettes/introduction-to-service.Rmd
@@ -19,7 +19,6 @@ knitr::opts_chunk$set(
 
 
 ```{r eval=FALSE}
-rm(list=ls())
 data("sample_analysis")
 data("skylineconfig")
 pp<-path.package("SRMService")

From bdaa2e0f10e612ff1071221cfb09028f35ae8c1c Mon Sep 17 00:00:00 2001
From: wolski <wewolski@gmail.com>
Date: Tue, 28 Apr 2020 11:23:02 +0200
Subject: [PATCH 3/6] remove rm(list=ls())

---
 .../RunScripts/RUN_VarSelection_Multinomial.R | 20 +++---
 .../Run_Generic_QuantTwoGroupAnalysis.R       | 62 ++++++++++++-------
 .../RunScripts/Run_MQ_QuantTwoGroupAnalysis.R | 53 +++++++++-------
 .../RunScripts/Run_PD_QuantTwoGroupAnalysis.R | 48 +++++++-------
 inst/RunScripts/Run_QuantQCReport.R           | 23 +++----
 inst/RunScripts/Run_VarSelection_GLM.R        | 52 +++++++++++-----
 inst/samples/proteinGroups/PullDownTest.R     | 54 +++++++++-------
 7 files changed, 187 insertions(+), 125 deletions(-)

diff --git a/inst/RunScripts/RUN_VarSelection_Multinomial.R b/inst/RunScripts/RUN_VarSelection_Multinomial.R
index 794e2aa..853cfb0 100644
--- a/inst/RunScripts/RUN_VarSelection_Multinomial.R
+++ b/inst/RunScripts/RUN_VarSelection_Multinomial.R
@@ -1,11 +1,14 @@
-rm(list=ls())
-
 library(SRMService)
 library(reshape2)
 
 packagedir <- path.package("SRMService")
-longm <- read.csv(file.path(packagedir, "samples/immunoLongFormat.txt"),row.names = 1,stringsAsFactors = F)
-longm$Intensity <- log2(longm$Intensity+1)
+longm <-
+  read.csv(
+    file.path(packagedir, "samples/immunoLongFormat.txt"),
+    row.names = 1,
+    stringsAsFactors = F
+  )
+longm$Intensity <- log2(longm$Intensity + 1)
 
 
 
@@ -13,7 +16,8 @@ longm$Intensity <- log2(longm$Intensity+1)
 longm$Protein <- longm$Variable
 protData <- ProteinVariableSelect$new(longm)
 
-rmarkdown::render("VariableSelection_MultinomialLasso.Rmd",output_format = "pdf_document", clean=FALSE)
-
-
-
+rmarkdown::render(
+  "VariableSelection_MultinomialLasso.Rmd",
+  output_format = "pdf_document",
+  clean = FALSE
+)
diff --git a/inst/RunScripts/Run_Generic_QuantTwoGroupAnalysis.R b/inst/RunScripts/Run_Generic_QuantTwoGroupAnalysis.R
index 2c9af27..b7610bc 100644
--- a/inst/RunScripts/Run_Generic_QuantTwoGroupAnalysis.R
+++ b/inst/RunScripts/Run_Generic_QuantTwoGroupAnalysis.R
@@ -4,14 +4,16 @@
 # www.github.com/protViz/SRMService
 # by W.E. Wolski, J. Grossmann, C. Panse
 #
-rm(list=ls())
 library(limma)
 library(SRMService)
 
 ### Protein groups file
 packagePath <- path.package("SRMService")
 packagePath <- "."
-proteinGroupsFile <- file.path(packagePath,"/inst/samples/genericQuantMatrix","Generic_QuantMatrix.txt")
+proteinGroupsFile <-
+  file.path(packagePath,
+            "/inst/samples/genericQuantMatrix",
+            "Generic_QuantMatrix.txt")
 
 # read in protein groups file
 protein <- readr::read_tsv(proteinGroupsFile)
@@ -29,35 +31,46 @@ colnames(protein) <- make.names(colnames(protein))
 originalHeaders <- colnames(protein)
 fakeNrPeptides <- rep(3, nrow(protein))
 fakeFastaHeader <- rep("No_Description", nrow(protein))
-protein <- cbind(protein,fakeNrPeptides, fakeFastaHeader)
+protein <- cbind(protein, fakeNrPeptides, fakeFastaHeader)
 
 
 # for project p2482 put the sample annotations from metainfo
-newHeaders <- c("Majority.protein.IDs", paste("Intensity.",originalHeaders[2:length(originalHeaders)], sep=""), "Peptides","Fasta.headers")
+newHeaders <-
+  c(
+    "Majority.protein.IDs",
+    paste("Intensity.", originalHeaders[2:length(originalHeaders)], sep = ""),
+    "Peptides",
+    "Fasta.headers"
+  )
 colnames(protein) <- newHeaders
 
 
 
 
 # all raw files in protein groups (select here for proper 2grp)
-rawF <- gsub("Intensity\\.", "", grep("Intensity\\.",colnames(protein),value=T) )
+rawF <-
+  gsub("Intensity\\.", "", grep("Intensity\\.", colnames(protein), value =
+                                  T))
 
 # how to parse condition from the filenames (separator in fn _ )
-condition <- quantable::split2table(rawF)[,3]
+condition <- quantable::split2table(rawF)[, 3]
 #
-annotation <- data.frame(Raw.file = rawF,
-                         Condition = condition,
-                         BioReplicate = paste("X",1:length(condition),sep=""),
-                         Run = 1:length(condition),
-                         IsotopeLabelType = rep("L",length(condition)),
-                         stringsAsFactors = F)
+annotation <- data.frame(
+  Raw.file = rawF,
+  Condition = condition,
+  BioReplicate = paste("X", 1:length(condition), sep =
+                         ""),
+  Run = 1:length(condition),
+  IsotopeLabelType = rep("L", length(condition)),
+  stringsAsFactors = F
+)
 
 
 ###################################
 ### Configuration section
 
 tmpdir <- tempdir()
-resultdir <- file.path(tmpdir,"GenericTwoGroup")
+resultdir <- file.path(tmpdir, "GenericTwoGroup")
 dir.create(resultdir)
 
 # calls up data editor
@@ -68,11 +81,11 @@ Experimentname = "pXXX_compareDifferentTissues"
 nrNas = sum(!is.na(annotation$Condition)) - 3
 
 nrPeptides = 2
-reference=unique(annotation$Condition)[1]
+reference = unique(annotation$Condition)[1]
 qvalueThreshold = 0.01
-qfoldchange =1
+qfoldchange = 1
 
-write.table(annotation, file=file.path(resultdir, "annotationused.txt"))
+write.table(annotation, file = file.path(resultdir, "annotationused.txt"))
 
 ####### END of user configuration ##
 
@@ -80,16 +93,17 @@ write.table(annotation, file=file.path(resultdir, "annotationused.txt"))
 # important structure for protein matrix
 
 # Do the analysis
-grp2 <- Grp2Analysis(annotation,
-                     Experimentname,
-                     maxNA=nrNas,
-                     nrPeptides=nrPeptides,
-                     reference=reference,
-                     numberOfProteinClusters = 20
-                     )
+grp2 <- Grp2Analysis(
+  annotation,
+  Experimentname,
+  maxNA = nrNas,
+  nrPeptides = nrPeptides,
+  reference = reference,
+  numberOfProteinClusters = 20
+)
 grp2$setMQProteinGroups(protein)
 
-grp2$setQValueThresholds(qvalue = qvalueThreshold,qfoldchange = qfoldchange)
+grp2$setQValueThresholds(qvalue = qvalueThreshold, qfoldchange = qfoldchange)
 
 #write out results and render pdf
 #readr::write_tsv(x = grp2$getResultTable(), path = file.path(resultdir,"pValues.csv"))
diff --git a/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R b/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R
index 9dbf259..4c69367 100644
--- a/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R
+++ b/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R
@@ -4,7 +4,6 @@
 # www.github.com/protViz/SRMService
 # by W.E. Wolski, J. Grossmann, C. Panse
 #
-rm(list=ls())
 library(limma)
 library(SRMService)
 
@@ -12,7 +11,8 @@ library(SRMService)
 packagedir <- path.package("SRMService")
 
 ####! set the path to the proteinGroups.txt file.
-proteinGroupsFile <- file.path(packagedir, "samples/proteinGroups/proteinGroups.txt")
+proteinGroupsFile <-
+  file.path(packagedir, "samples/proteinGroups/proteinGroups.txt")
 
 ###
 
@@ -20,22 +20,28 @@ proteinGroupsFile <- file.path(packagedir, "samples/proteinGroups/proteinGroups.
 protein <- readr::read_tsv(proteinGroupsFile)
 colnames(protein) <- make.names(colnames(protein))
 tmp <- cumsum(rev(table(protein$Peptides)))
-barplot(tmp[(length(tmp)-5):length(tmp)],ylim=c(0, length(protein$Peptides)),xlab='nr of proteins with at least # peptides')
+barplot(tmp[(length(tmp) - 5):length(tmp)], ylim = c(0, length(protein$Peptides)), xlab =
+          'nr of proteins with at least # peptides')
 
 ##
-rawF <- gsub("Intensity\\.", "", grep("Intensity\\.",colnames(protein),value=T) )
+rawF <-
+  gsub("Intensity\\.", "", grep("Intensity\\.", colnames(protein), value =
+                                  T))
 
-condition <- quantable::split2table(rawF)[,3]
+condition <- quantable::split2table(rawF)[, 3]
 
 # Raw.file <- c("23bb","23bcd","23ddd","","","")
 # condition <- c("baseline","baseline","w1","w1")
 
-annotation <- data.frame(Raw.file = rawF,
-                         Condition = condition,
-                         BioReplicate = paste("X",1:length(condition),sep=""),
-                         Run = 1:length(condition),
-                         IsotopeLabelType = rep("L",length(condition)),
-                         stringsAsFactors = F)
+annotation <- data.frame(
+  Raw.file = rawF,
+  Condition = condition,
+  BioReplicate = paste("X", 1:length(condition), sep =
+                         ""),
+  Run = 1:length(condition),
+  IsotopeLabelType = rep("L", length(condition)),
+  stringsAsFactors = F
+)
 
 
 
@@ -50,26 +56,28 @@ Experimentname = ""
 nrNas = sum(!is.na(annotation$Condition)) - 1
 nrNas = 5
 nrPeptides = 2
-reference=unique(annotation$Condition)[1]
-reference="WT"
+reference = unique(annotation$Condition)[1]
+reference = "WT"
 qvalueThreshold = 0.05
-qfoldchange =1
-write.table(annotation, file=file.path(resultdir, "annotationused.txt"))
+qfoldchange = 1
+write.table(annotation, file = file.path(resultdir, "annotationused.txt"))
 
 ####### END of user configuration ##
 
 # source("R/Grp2Analysis.R")
-grp2 <- Grp2Analysis(annotation, "Experimentname",
-                     maxNA=nrNas,
-                     nrPeptides=nrPeptides,
-                     reference=reference,
-                     numberOfProteinClusters = 20
-                     )
+grp2 <- Grp2Analysis(
+  annotation,
+  "Experimentname",
+  maxNA = nrNas,
+  nrPeptides = nrPeptides,
+  reference = reference,
+  numberOfProteinClusters = 20
+)
 
 grp2$getDesignMatrix()
 
 grp2$setMQProteinGroups(protein)
-grp2$setQValueThresholds(qvalue = qvalueThreshold,qfoldchange = qfoldchange)
+grp2$setQValueThresholds(qvalue = qvalueThreshold, qfoldchange = qfoldchange)
 mqQuantMatrixGRP2 <- grp2
 
 head(mqQuantMatrixGRP2$getModPValuesCI())
@@ -80,4 +88,3 @@ usethis::use_data(mqQuantMatrixGRP2, overwrite = TRUE)
 ## REMOVE TO RENDER
 # rmarkdown::render("vignettes/Grp2AnalysisHeatmap3.Rmd",bookdown::pdf_document2(), params=list(grp = grp2))
 # rmarkdown::render("vignettes/Grp2Analysis.Rmd",bookdown::pdf_document2(), params=list(grp = grp2))
-
diff --git a/inst/RunScripts/Run_PD_QuantTwoGroupAnalysis.R b/inst/RunScripts/Run_PD_QuantTwoGroupAnalysis.R
index 9cd1fdc..e79605d 100644
--- a/inst/RunScripts/Run_PD_QuantTwoGroupAnalysis.R
+++ b/inst/RunScripts/Run_PD_QuantTwoGroupAnalysis.R
@@ -4,26 +4,29 @@ library(quantable)
 library(SRMService)
 
 ## specify file names
+
 inputFilesFile <- "20161115_02_G3_InputFiles.txt"
 proteinsFile <- "20161115_02_G3_Proteins.txt"
 ##
 
 
-rm(list=ls())
-inputFiles <- read_tsv( inputFilesFile )
+inputFiles <- read_tsv(inputFilesFile)
 inputFileFix <- fix_PD_inputFiles(inputFiles)
 
-annotation <- data.frame(Raw.file = inputFileFix$Raw.File,
-                         Condition = gsub("[0-9]","",quantable::split2table(inputFileFix$Raw.File)[,3]),
-                         BioReplicate = paste("X",1:nrow(inputFileFix),sep=""),
-                         Run = 1:nrow(inputFileFix),
-                         IsotopeLabelType = rep("L",nrow(inputFileFix)),
-                         stringsAsFactors = F)
+annotation <- data.frame(
+  Raw.file = inputFileFix$Raw.File,
+  Condition = gsub("[0-9]", "", quantable::split2table(inputFileFix$Raw.File)[, 3]),
+  BioReplicate = paste("X", 1:nrow(inputFileFix), sep =
+                         ""),
+  Run = 1:nrow(inputFileFix),
+  IsotopeLabelType = rep("L", nrow(inputFileFix)),
+  stringsAsFactors = F
+)
 
 
 
-proteins <- read_tsv( proteinsFile )
-proteinsFIX <- remap_PD_ProteinTable(proteins,inputFiles)
+proteins <- read_tsv(proteinsFile)
+proteinsFIX <- remap_PD_ProteinTable(proteins, inputFiles)
 
 
 
@@ -31,32 +34,35 @@ proteinsFIX <- remap_PD_ProteinTable(proteins,inputFiles)
 ###################################
 ### Configuration section
 fix(annotation)
-resultdir="output"
+resultdir = "output"
 dir.create(resultdir)
 
 
 Experimentname = ""
 nrNas = sum(!is.na(annotation$Condition)) - 1
 nrPeptides = 2
-reference=unique(annotation$Condition)[1]
+reference = unique(annotation$Condition)[1]
 qvalueThreshold = 0.01
-qfoldchange =2
+qfoldchange = 2
 
-write.table(annotation, file=file.path(resultdir, "annotationused.txt"))
+write.table(annotation, file = file.path(resultdir, "annotationused.txt"))
 
 ####### END of user configuration ##
 
 
 
 library(SRMService)
-grp2 <- Grp2Analysis(annotation, "test pd import", maxNA=nrNas  , nrPeptides=nrPeptides, reference=reference)
+grp2 <-
+  Grp2Analysis(
+    annotation,
+    "test pd import",
+    maxNA = nrNas  ,
+    nrPeptides = nrPeptides,
+    reference = reference
+  )
 grp2$setProteins(proteinsFIX)
-grp2$setQValueThresholds(qvalue = qvalueThreshold,qfoldchange = qfoldchange)
+grp2$setQValueThresholds(qvalue = qvalueThreshold, qfoldchange = qfoldchange)
 
 results <- grp2$getResultTableWithPseudo()
-write_tsv(results,path= file.path(resultdir,"pValues.tsv"))
+write_tsv(results, path = file.path(resultdir, "pValues.tsv"))
 rmarkdown::render("Grp2Analysis.Rmd", output_format = bookdown::pdf_document2())
-
-
-
-
diff --git a/inst/RunScripts/Run_QuantQCReport.R b/inst/RunScripts/Run_QuantQCReport.R
index d407f37..8cea010 100644
--- a/inst/RunScripts/Run_QuantQCReport.R
+++ b/inst/RunScripts/Run_QuantQCReport.R
@@ -7,7 +7,6 @@
 
 #
 
-rm(list=ls())
 library(reshape2)
 library(limma)
 library(SRMService)
@@ -16,7 +15,7 @@ library(SRMService)
 # max na per protein
 maxNA <- 3
 # min number of peptides per protein
-nrPeptides <-2
+nrPeptides <- 2
 # Experiment name (will appear as title in the pdf)
 experimentName <- "myTesting"
 
@@ -24,19 +23,21 @@ experimentName <- "myTesting"
 
 
 ### Do not edit (except you know what you are doing)
-protein <- read.table("proteinGroups.txt",
-                      sep="\t",
-                      stringsAsFactors = F,
-                      header=T)
+protein <- read.table(
+  "proteinGroups.txt",
+  sep = "\t",
+  stringsAsFactors = F,
+  header = T
+)
 
 tmp <- cumsum(rev(table(protein$Peptides)))
-barplot(tmp[(length(tmp)-5):length(tmp)],ylim=c(0, length(protein$Peptides)),xlab='nr of proteins with at least # peptides')
+barplot(tmp[(length(tmp) - 5):length(tmp)], ylim = c(0, length(protein$Peptides)), xlab =
+          'nr of proteins with at least # peptides')
 
-grp2 <- QCProteinReport(experimentName, maxNA=maxNA  , nrPeptides=nrPeptides)
+grp2 <-
+  QCProteinReport(experimentName, maxNA = maxNA  , nrPeptides = nrPeptides)
 grp2$setMQProteinGroups(protein)
 
 
 #rmarkdown::render("QCReport.Rmd","pdf_document")
-rmarkdown::render("QCReport.Rmd",bookdown::pdf_document2())
-
-
+rmarkdown::render("QCReport.Rmd", bookdown::pdf_document2())
diff --git a/inst/RunScripts/Run_VarSelection_GLM.R b/inst/RunScripts/Run_VarSelection_GLM.R
index 4da44c9..1194206 100644
--- a/inst/RunScripts/Run_VarSelection_GLM.R
+++ b/inst/RunScripts/Run_VarSelection_GLM.R
@@ -1,4 +1,3 @@
-rm(list=ls())
 library(reshape2)
 library(plyr)
 library(dplyr)
@@ -8,14 +7,21 @@ library(SRMService)
 
 
 packagedir <- path.package("SRMService")
-longm <- read.csv(file.path(packagedir, "samples/immunoLongFormat.txt"),row.names = 1,stringsAsFactors = F)
-
-longm$Intensity <- log2(longm$Intensity+1)
+longm <-
+  read.csv(
+    file.path(packagedir, "samples/immunoLongFormat.txt"),
+    row.names = 1,
+    stringsAsFactors = F
+  )
+
+longm$Intensity <- log2(longm$Intensity + 1)
 longm$Protein <- longm$Variable
 
 
-data2Conditions$Condition[data2Conditions$Condition == "Healthy" | data2Conditions$Condition == "Gingivitis"] <- "NonPeriodontitis"
-data2Conditions$Condition[(data2Conditions$Condition == "Aggressive" | data2Conditions$Condition == "Chronic")] <- "Periodontitis"
+data2Conditions$Condition[data2Conditions$Condition == "Healthy" |
+                            data2Conditions$Condition == "Gingivitis"] <- "NonPeriodontitis"
+data2Conditions$Condition[(data2Conditions$Condition == "Aggressive" |
+                             data2Conditions$Condition == "Chronic")] <- "Periodontitis"
 
 unique(data2Conditions$Condition)
 
@@ -23,21 +29,35 @@ protData <- Protein$new(data2Conditions)
 
 
 comparisonName <- "Periodontitis vs NonPeriodontitis"
-rmarkdown::render("VariableSelection_ROCSingleProtein.Rmd", output_format = "html_document",
-                  output_file = paste("ROC2GroupPeriodontitisVSNon.html",sep=""), clean = FALSE)
-rmarkdown::render("VariableSelection_ROCSingleProtein.Rmd", output_format = "pdf_document",
-                  output_file = paste("ROC2GroupPeriodontitisVSNon.pdf",sep="") , clean = FALSE)
+rmarkdown::render(
+  "VariableSelection_ROCSingleProtein.Rmd",
+  output_format = "html_document",
+  output_file = paste("ROC2GroupPeriodontitisVSNon.html", sep =
+                        ""),
+  clean = FALSE
+)
+rmarkdown::render(
+  "VariableSelection_ROCSingleProtein.Rmd",
+  output_format = "pdf_document",
+  output_file = paste("ROC2GroupPeriodontitisVSNon.pdf", sep =
+                        "") ,
+  clean = FALSE
+)
 
 
 tmplong <- longm
-nvariables <-3
+nvariables <- 3
 
 
 Condition2Compare <- "NonPeriodontitis"
 
 rmarkdown::render("VariableSelection_GLM.Rmd",
-                  output_file = "SelectVarsNonParandonditisVSParandontitis.html", clean = FALSE)
-
-rmarkdown::render("VariableSelection_GLM.Rmd", output_format = "pdf_document",
-                  output_file = "SelectVarsNonParandonditisVSParandontitis.pdf", clean=FALSE)
-
+                  output_file = "SelectVarsNonParandonditisVSParandontitis.html",
+                  clean = FALSE)
+
+rmarkdown::render(
+  "VariableSelection_GLM.Rmd",
+  output_format = "pdf_document",
+  output_file = "SelectVarsNonParandonditisVSParandontitis.pdf",
+  clean = FALSE
+)
diff --git a/inst/samples/proteinGroups/PullDownTest.R b/inst/samples/proteinGroups/PullDownTest.R
index 25dfac9..3d853dc 100644
--- a/inst/samples/proteinGroups/PullDownTest.R
+++ b/inst/samples/proteinGroups/PullDownTest.R
@@ -4,36 +4,44 @@
 # www.github.com/protViz/SRMService
 # by W.E. Wolski, J. Grossmann, C. Panse
 #
-rm(list=ls())
 library(limma)
 library(SRMService)
 
-protein <- system.file("samples/proteinGroups/proteinGroupsPullDown.txt",package = "SRMService")
+protein <-
+  system.file("samples/proteinGroups/proteinGroupsPullDown.txt", package = "SRMService")
 protein <- readr::read_tsv(protein)
 colnames(protein) <- make.names(colnames(protein))
 
 
-tmp <- strsplit(protein$Majority.protein.IDs,split=" ")
-tmp2 <- sapply(tmp, function(x){x[1]})
-protein$Majority.protein.IDs <- gsub(">","",tmp2)
+tmp <- strsplit(protein$Majority.protein.IDs, split = " ")
+tmp2 <- sapply(tmp, function(x) {
+  x[1]
+})
+protein$Majority.protein.IDs <- gsub(">", "", tmp2)
 
 
-rawF <- gsub("Intensity\\.", "", grep("Intensity\\.",colnames(protein),value=T) )
+rawF <-
+  gsub("Intensity\\.", "", grep("Intensity\\.", colnames(protein), value =
+                                  T))
 condition <- quantable::split2table(rawF)
-condition <- paste(condition[,4], condition[,5], sep="_")
-annotation <- data.frame(Raw.file = rawF,
-                         Condition = condition,
-                         BioReplicate = paste("X",1:length(condition),sep=""),
-                         Run = 1:length(condition),
-                         IsotopeLabelType = rep("L",length(condition)),
-                         stringsAsFactors = F)
+condition <- paste(condition[, 4], condition[, 5], sep = "_")
+annotation <- data.frame(
+  Raw.file = rawF,
+  Condition = condition,
+  BioReplicate = paste("X", 1:length(condition), sep =
+                         ""),
+  Run = 1:length(condition),
+  IsotopeLabelType = rep("L", length(condition)),
+  stringsAsFactors = F
+)
 
 
 workdir <- "output"
 dir.create(workdir)
 
 tmp <- cumsum(rev(table(protein$Peptides)))
-barplot(tmp[(length(tmp)-5):length(tmp)],ylim=c(0, length(protein$Peptides)),xlab='nr of proteins with at least # peptides')
+barplot(tmp[(length(tmp) - 5):length(tmp)], ylim = c(0, length(protein$Peptides)), xlab =
+          'nr of proteins with at least # peptides')
 
 ###################################
 ### Configuration section
@@ -42,19 +50,21 @@ Experimentname = "p2550"
 nrNas = 5
 nrPeptides = 2
 
-annotation$Condition[grepl("_w$",annotation$Condition)] <- NA
+annotation$Condition[grepl("_w$", annotation$Condition)] <- NA
 reference = "pegfp_wo" # unique(annotation$Condition)[3]
 
 #write.table(annotation, file="output/annotationused.txt")
 
 
 ####### END of user configuration ##
-grp2 <- Grp2Analysis(annotation, "Experimentname",
-                     maxNA=nrNas,
-                     nrPeptides=nrPeptides,
-                     reference=reference,
-                     numberOfProteinClusters = 20
-                     )
+grp2 <- Grp2Analysis(
+  annotation,
+  "Experimentname",
+  maxNA = nrNas,
+  nrPeptides = nrPeptides,
+  reference = reference,
+  numberOfProteinClusters = 20
+)
 grp2$setMQProteinGroups(protein)
 grp2$qfoldchange = 2
 grp2$setQValueThresholds(qvalue = 0.01)
@@ -63,7 +73,7 @@ grp2PullDownExample <- grp2
 
 x2 <- grp2$getResultTable()
 dim(x2)
-x3 <-grp2$getResultTableWithPseudo()
+x3 <- grp2$getResultTableWithPseudo()
 dim(x3)
 
 usethis::use_data(grp2PullDownExample, overwrite = TRUE)

From 72eb0a0368a9325ab15680fc024d21cc994dc33b Mon Sep 17 00:00:00 2001
From: jjGG <jg@fgcz.ethz.ch>
Date: Tue, 17 Dec 2019 12:15:06 +0100
Subject: [PATCH 4/6] not needed here

---
 .DS_Store                 | Bin 10244 -> 10244 bytes
 output/annotationused.txt |  13 -------------
 2 files changed, 13 deletions(-)
 delete mode 100644 output/annotationused.txt

diff --git a/.DS_Store b/.DS_Store
index abeca4abbb70685d680d09064d9fbd24b747319a..961c4b0f719df5dce4ff1141d822fcb79ffc1519 100644
GIT binary patch
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diff --git a/output/annotationused.txt b/output/annotationused.txt
deleted file mode 100644
index f7e8086..0000000
--- a/output/annotationused.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-"Raw.file" "Condition" "BioReplicate" "Run" "IsotopeLabelType"
-"1" "20160217_02_WT_4_rep2" "WT" "X1" 1 "L"
-"2" "20160217_03_WT_2_rep" "WT" "X2" 2 "L"
-"3" "20160217_04_KO_3" "KO" "X3" 3 "L"
-"4" "20160217_05_KO_2" "KO" "X4" 4 "L"
-"5" "20160217_07_WT_1" "WT" "X5" 5 "L"
-"6" "20160217_08_KO_5" "KO" "X6" 6 "L"
-"7" "20160217_09_WT_5" "WT" "X7" 7 "L"
-"8" "20160217_10_WT_3_rep" "WT" "X8" 8 "L"
-"9" "20160217_12_WT_6_rep" "WT" "X9" 9 "L"
-"10" "20160217_13_KO_1_rep" "KO" "X10" 10 "L"
-"11" "20160217_14_KO_4" "KO" "X11" 11 "L"
-"12" "20160217_15_KO_6" "KO" "X12" 12 "L"

From be680b7527ae7c97beec2c59804bf05228aebe7f Mon Sep 17 00:00:00 2001
From: jjGG <jg@fgcz.ethz.ch>
Date: Mon, 31 Aug 2020 12:21:34 +0200
Subject: [PATCH 5/6] BSmac file (ds_store)

---
 .DS_Store | Bin 10244 -> 10244 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/.DS_Store b/.DS_Store
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From d179740adea9ef50ada26b0731d5700171d2c91b Mon Sep 17 00:00:00 2001
From: Witold Wolski <wewolski@gmail.com>
Date: Tue, 27 Oct 2020 09:30:31 +0100
Subject: [PATCH 6/6] Update README.md

---
 README.md | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index a1948e1..346ea83 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,24 @@ For more information about this project please visit the wproject wiki
 
 
 ## Install
+For Debian 10
+You will need to have installed:
+
+```
+sudo apt-get install libssl-dev
+sudo apt-get install pandoc
+sudo apt-get isntall pandoc-citeproc
+```
+
+
+```{r}
+install.packages(c("bookdown", "conflicted", "corrplot", "dplyr", "forcats", "gridExtra", "heatmap3", "limma", "missForest", "pander", "plyr", "purrr", "quantable", "R6", "reshape2", "rlang", "rmarkdown", "scales", "shiny", "tibble", "tidyr", "tidyverse", "usethis"))
+install.packages(c("tidyverse","usethis"))
+
+install.packages("BiocManager")
+BiocManager::install("limma")
+```
+
 
 ```{r}
 library(devtools)
@@ -13,7 +31,9 @@ install_github(c('protViz/SRMService'))
 ```
 
 
-## Deployment on server
+## Deployment on shiny-server
+
+
 
 
 ```{r}