inst/doc/skin_muscle_preprocessing.R

In rmflight/ccPaper: work for categoryCompare paper revisions

## ----customCSS, include=FALSE--------------------------------------------
cssFile <- system.file("extdata", "style.css", package="ccPaper")
options(markdown.HTML.stylesheet = cssFile)


## ----loadLibrary, message=FALSE------------------------------------------
library(ccPaper)


## ----loadLibraries-------------------------------------------------------
options(stringsAsFactors=FALSE)
library(affy)


## ----skinRaw, eval=FALSE-------------------------------------------------
## currLoc <- getwd()
## dataLoc <- "/mlab/data/rmflight/Documents/projects/work/Petruska/drg_sc_skin_denervation/Skin/"
## setwd(dataLoc)
## 
## attFile <- "Sample information file.txt"
## dataAttributes <- read.table(attFile, sep="\t", header=T)
## dataAttributes$timePoint <- 0
## dataAttributes$timePoint[(dataAttributes$Time == "7 day")] <- 7
## dataAttributes$timePoint[(dataAttributes$Time == "14 day")] <- 14
## 
## celData <- ReadAffy(phenoData=dataAttributes)
## skinData <- rma(celData)
## 
## setwd(currLoc)
## .sessionInfo <- sessionInfo()
## .timeDate <- Sys.time()
## save(skinData, .sessionInfo, .timeDate, file="inst/data/skin_rma_data.RData")


## ----muscleRaw, eval=FALSE-----------------------------------------------
## library(GEOquery)
## muscleData <- getGEO(GEO="GSE4411")[[1]]
## 
## controlSamples <- grep("Control", pData(muscleData)$title)
## muscleData <- muscleData[,controlSamples]
## 
## tmpP <- pData(muscleData)
## tmpP$innervation <- "innervated"
## denLoc <- grep("Denervated", tmpP$title)
## tmpP$innervation[denLoc] <- "denervated"
## pData(muscleData) <- tmpP
## .sessionInfo <- sessionInfo()
## .timeDate <- Sys.time()
## save(muscleData, .sessionInfo, .timeDate, file="inst/data/muscle_data.RData")


## ----diffSkin------------------------------------------------------------
library(limma)
library(rat2302.db)
data(skin_rma_data)

skinComps <- c("T7 - T0", "T14 - T0")
geneID <- unlist(mget(featureNames(skinData), rat2302ENTREZID))

skinExpr <- exprs(skinData)
skinCollapse <- collapseProbes(skinExpr, geneID) # collapse to single genes using median of expression
skinCharacter <- pData(skinData)
skinCharacter$timePoint2 <- paste("T", skinCharacter$timePoint, sep="")

skinFC <- rankGenes(skinCollapse, skinCharacter$timePoint2, skinComps, doAggregation=FALSE, aggregateIndex=NA)
names(skinFC) <- c("T7", "T14")

skinDiff <- lapply(skinFC, getDiffGenes, id="id")


## ----setupGeneSets-------------------------------------------------------
library(GO.db)
library(org.Rn.eg.db)
library(limma)
rnGO <- as.list(org.Rn.egGO2ALLEGS)
rnGO <- rnGO[(Ontology(names(rnGO)) == "BP")]
rnGO <- lapply(rnGO, unique)

skinSet <- symbols2indices(rnGO, rownames(skinCollapse))


## ----skinContrasts, eval=FALSE-------------------------------------------
## skinStatus <- skinCharacter$timePoint2
## f <- factor(skinStatus)
## skinDesign <- model.matrix(~0 + f)
## colnames(skinDesign) <- levels(f)
## 
## skinContrast <- makeContrasts(contrasts=skinComps, levels=skinDesign)
## 
## save(list=ls(), file="runSkinRomer.RData")


## ----skinRomer, eval=FALSE-----------------------------------------------
## load("runSkinRomer.RData")
## options(mc.cores=12) # at least if we are on hera
## t1 <- Sys.time()
## skinRomer <- multicontrastRomer(skinSet, skinCollapse, skinDesign, skinContrast, nrot=10000)
## names(skinRomer) <- c("T7", "T14")
## save(skinRomer, file="inst/data/skinRomer.RData")
## t2 <- Sys.time()
## difftime(t2, t1)


## ----runGeneSetTest, eval=FALSE------------------------------------------
## load("runSkinRomer.RData")
## options(mc.cores=12) # at least if we are on hera
## t1 <- Sys.time()
## skinGeneSetTest <- lapply(skinFC, function(x){
##   mmGeneSetTest(skinSet, x$t)
## })
## 
## t2 <- Sys.time()
## difftime(t2, t1)
## save(skinGeneSetTest, t1, t2, file="inst/data/skinGeneSetTest.RData")


## ----diffMuscle----------------------------------------------------------
library(limma)
library(mouse4302.db)
data(muscle_data)

muscleComps <- c("denervated - innervated")
geneID <- unlist(mget(featureNames(muscleData), mouse4302ENTREZID))

muscleExpr <- exprs(muscleData)
muscleCollapse <- collapseProbes(muscleExpr, geneID) # collapse to single genes using median of expression
muscleCharacter <- pData(muscleData)

muscleFC <- rankGenes(muscleCollapse, muscleCharacter$innervation, muscleComps, doAggregation=FALSE, aggregateIndex=NA)
names(muscleFC) <- "denervation"

muscleDiff <- lapply(muscleFC, getDiffGenes, id="id")


## ----setupGeneSetsMuscle-------------------------------------------------
library(GO.db)
library(org.Mm.eg.db)
library(limma)
mmGO <- as.list(org.Mm.egGO2ALLEGS)
mmGO <- mmGO[(Ontology(names(mmGO)) == "BP")]
mmGO <- lapply(mmGO, unique)

muscleSet <- symbols2indices(mmGO, rownames(muscleCollapse))


## ----muscleContrasts, eval=FALSE-----------------------------------------
## muscleStatus <- muscleCharacter$innervation
## f <- factor(muscleStatus)
## muscleDesign <- model.matrix(~0 + f)
## colnames(muscleDesign) <- levels(f)
## 
## muscleContrast <- makeContrasts(contrasts=muscleComps, levels=muscleDesign)
## 
## save(muscleSet, muscleCollapse, muscleDesign, muscleContrast, mmGO, muscleFC, file="runMuscleRomer.RData")


## ----muscleRomer, eval=FALSE---------------------------------------------
## load("runMuscleRomer.RData")
## options(mc.cores=12) # at least if we are on hera
## t1 <- Sys.time()
## muscleRomer <- multicontrastRomer(muscleSet, muscleCollapse, muscleDesign, muscleContrast, nrot=10000)
## names(muscleRomer) <- "denervation"
## save(muscleRomer, file="inst/data/muscleRomer.RData")
## t2 <- Sys.time()
## difftime(t2, t1)


## ----getDataOut----------------------------------------------------------
data(muscleRomer)
data(skinRomer)

bothGO <- union(names(rnGO), names(mmGO))
combMapping <- lapply(bothGO, function(inName){
  isMM <- inName %in% names(mmGO)
  isRN <- inName %in% names(rnGO)
  
  tmpGene <- character(0)
  
  if (isMM){
    tmpGene <- c(tmpGene, mmGO[[inName]])
  }
  if (isRN){
    tmpGene <- c(tmpGene, rnGO[[inName]])
  }
  tmpGene <- unique(tmpGene)
  return(tmpGene)
})

names(combMapping) <- bothGO

geneAnnMapping <- new("namedList", .Data=combMapping, names=names(combMapping))


getSigID <- function(inRomer, pCut=0.05, whichCol=c("Up", "Down")){
  sigID <- lapply(whichCol, function(inCol){
    rownames(inRomer[(inRomer[, inCol] <= pCut),])
  })
  names(sigID) <- whichCol
  return(sigID)
}

muscleSigRomer <- lapply(muscleRomer, getSigID, pCut=0.01)
muscleSigRomer <- unlist(muscleSigRomer, recursive=FALSE)
names(muscleSigRomer) <- c("muscle.Up", "muscle.Down")

skinSigRomer <- lapply(skinRomer, getSigID, pCut = 0.01)
skinSigRomer <- unlist(skinSigRomer, recursive=FALSE)

allSigRomer <- c(skinSigRomer, muscleSigRomer)

genCCSigList <- function(inSig){
  tmp <- new("ccSigList", sigID=inSig)
}

allCCSig <- lapply(allSigRomer, genCCSigList)

allCCRomer <- new("GENccEnrichResult", allCCSig, categoryName="GSEAGO", geneAnnMapping=geneAnnMapping, overlapType="overlap", annDescription=Term(names(geneAnnMapping)))

allRomerOpts <- new("ccOptions", listNames=names(allCCRomer), colorType="pie")
compareSMRomer <- ccCompare(allCCRomer, allRomerOpts)
compareSMRomer


## ----saveData, eval=FALSE------------------------------------------------
## save(compareSMRomer, allRomerOpts, file="skinMuscleCompare.RData")


## ----out2cytoscape, eval=FALSE-------------------------------------------
## compareSMRomer <- breakEdges(compareSMRomer, 0.8)
## cwSM <- ccOutCyt(compareSMRomer, allRomerOpts, postText="GSEAGO", rpcPort=9001)


## ----saveCytResults, eval=FALSE------------------------------------------
## .sessionInfo <- sessionInfo()
## .timeDate <- Sys.time()
## save(cwSM, compareSMRomer, allRomerOpts, .sessionInfo, .timeDate, file="inst/data/skinMuscleCompareOutput.RData")


## ----outGOTerms, eval=FALSE----------------------------------------------
## smNodes <- cytOutNodes("typeII hypersensitivity - T7.Up", cwSM)
## smNodes <- cytOutNodes("pH and lysosome regulation - Skin.T7.Down,Skin.T14.Up,Muscle.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("Neurotransmitter secretion and transport - Skin.T7.Down,Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("entry into host and movement - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("steriod biosynthesis - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("microtubule organization - Skin.T7.Up,Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("cellular respiration - Skin.T14.Down,Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("epithelial tube branching - Skin.T7.Down,Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("rRNA processing - Muscle.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("digestion - Skin.T14.Up", cwWM, smNodes)
## smNodes <- cytOutNodes("digestion - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("response to virus - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("purine metabolism - Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("protein localization in mitochondrion - Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("synapse assembly and nervous system development - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("folic acid compound metabolism - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("retinoic acid biosynthesis - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("mitotic spindle assembly - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("regulation of phospholipase C - Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("acetyl CoA biosynthesis - Skin.T14.Down,Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("response to glucose - Skin.T7.Down, Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("response to VEGF - Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("mitotic cell cycle checkpoint - Skin.T7.Down,Skin.T14.Down,Muscle.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("urea cycle - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("response to prostaglandin - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("keratinocyte migration - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("atp biosynthesis - Skin.T7.Down,Skin.T14.Down,Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("membrane repolarization - Muscle.Down", cwSM, smNodes)
## smNOdes <- cytOutNodes("muscle contraction and development - Skin.T7.Down,Skin.T14.Down,Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("muscle contraction and development - Skin.T7.Down,Skin.T14.Down,Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("muscle contraction and development - Skin.T7.Down,Skin.T14.Down,Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("blood vessel endothelial cell differentiation - Skin.T7.Up,Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("endocrine regulation of blood pressure - Skin.T7.Down,Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("tube development - Skin.T7.Down,Muscle.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("amino acid transport - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("cation channel activity - Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("interferon gamma response - Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("lung cell differentiation - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("neg regulation of astrocyte diff. - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("fear response - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("N acetylglucosamine metabolism - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("proteoglycan biosynthesis - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("carbohydrate catabolism - Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("response to muscle activity - Skin.T14.Down,Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("response to indole 3 methanol - Muscle.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("negative regulation of response to granulocyte / myeloid cell diff. - Skin.T7.Up,Muscle.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("vitamin metabolism - Skin.T14.Up,Muscle.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("DNA break repair - Muscle.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("calcineurin NFAT signaling cascade - Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("histone demethylation - Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("negative regulation of Ras signal transduction - Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("positive regulation of metalloenzyme activity - Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("glucocorticoid receptor signaling pathway - Skin.T14.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("mesenchymal cell diff in kidney / renal system dev. - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("axon extension - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("lung lobe dev. and morphogenesis - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("embryonic digestive tract dev. and morphogenesis - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("negative regulation of protein transport - Skin.T7.Up,Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("phosphate ion transport - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("fluid transport - Skin.T7.Down,Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("fluid secretion - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("interleukin 13 production - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("glia guided migration - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("central nervous system maturation - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("bile acid transport - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("positive regulation of muscle cell apoptosis - Skin.T14.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("atrioventricular valve dev. and morphogenesis - Skin.T14.Up,Muscle.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("dopamine transport - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("collateral sprouting - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("response to osmotic stress - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("positive regulation of epidermal growth factor signaling - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("response to leptin - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("catecholamin biosynthesis - Skin.T7.Down", cwSM, smNodes)
## smNodes <- cytOutNodes("negative regulation of cell junction assembly - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("endocardial cell differentiation - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("sequestering of actin monomers - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("beta amyloid formation - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("response to platelet derived growth factor stimulus - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("lipopolysaccharid biosynthesis - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("aminoglycan metabolism - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("epithelial to mesenchymal transition, endocardial cushion formation - Skin.T7.Up", cwSM, smNodes)
## smNodes <- cytOutNodes("pulmonary valve dev. and morphogenesis - Skin.T7.Up", cwSM, smNodes)
## .sessionInfo <- sessionInfo()
## .timeDate <- Sys.time()
## save(smNodes, cwSM, allCCRomer, allRomerOpts, compareSMRomer, file="inst/data/skinMuscleCCOutput.RData")


## ----genTableOutput------------------------------------------------------
data(skinMuscleCCOutput)

allDescStrings <- sapply(smNodes, function(x){x$descStr})
string2List <- strsplit(allDescStrings, " - ", fixed=TRUE)
justDesc <- sapply(string2List, function(x){x[1]})
listMem <- sapply(string2List, function(x){x[2]})
listMem[1] <- "Skin.T7.Up" # fix an error in the initial setup
listMemSplit <- strsplit(listMem, ",", fixed=TRUE)

descMembershipTable <- matrix("", nrow=length(allDescStrings), ncol=7)
colnames(descMembershipTable) <- c("Description", "Skin.T7.Down", "Skin.T7.Up", "Skin.T14.Down", "Skin.T14.Up", "Muscle.Down", "Muscle.Up")

descMembershipTable[,"Description"] <- justDesc

for (inRow in seq(1, nrow(descMembershipTable))){
  useSplit <- listMemSplit[[inRow]]
  trimSplit <- gsub(" ", "", useSplit)
  descMembershipTable[inRow, trimSplit] <- "X"
}

orderBy <- c("Skin.T7.Down,Skin.T14.Down,Muscle.Down",
             "Skin.T7.Down,Skin.T14.Down,Muscle.Up",
             "Skin.T7.Down,Skin.T14.Down",
             "Skin.T7.Down,Skin.T14.Up,Muscle.Up",
             "Skin.T7.Down,Skin.T14.Up",
             "Skin.T7.Down,Muscle.Up",
             "Skin.T7.Down,Muscle.Down",
             "Skin.T7.Down",
             "Skin.T7.Up,Skin.T14.Down",
             "Skin.T7.Up,Skin.T14.Up",
             "Skin.T7.Up,Muscle.Up",
             "Skin.T7.Up",
             "Skin.T14.Down,Muscle.Down",
             "Skin.T14.Down",
             "Skin.T14.Up,Muscle.Down",
             "Skin.T14.Up,Muscle.Up",
             "Skin.T14.Up",
             "Muscle.Down",
             "Muscle.Up")

listMem <- gsub(" ", "", listMem)
newOrder <- unlist(lapply(orderBy, function(x){
  which(listMem %in% x)
}))

descMembershipTable <- descMembershipTable[newOrder,]
require(xtable)

# add an html link to each entry in the table
useLink <- paste('<a href="#loc', seq(1, nrow(descMembershipTable)), '">', descMembershipTable[,"Description"], '</a>', sep="")
descMembershipTable[, "Description"] <- useLink


## ----printTable, echo=FALSE, results='asis'------------------------------
cat('<a name="tableLink"></a>\n') # a link back to the table
print(xtable(descMembershipTable), type = 'html', html.table.attributes = 'style="border-spacing:20px 5px;"', include.rownames=FALSE, sanitize.text.function=function(x){x})


## ----detailTable, echo=FALSE, results='asis'-----------------------------
smNodes <- smNodes[newOrder]

for (iNode in seq(1:length(smNodes))){
  nodeSet <- smNodes[[iNode]]
  toLink <- paste('<a name="loc', iNode, '"></a>', sep="")
  cat(toLink, "\n")
  cat("####", nodeSet$descStr, sep=" ")
  cat("\n")
  
  nGO <- length(nodeSet$nodes)
  outMatrix <- matrix("", nrow=nGO, ncol=8)
  colnames(outMatrix) <- c("GOID", "Description", "T7.Down", "T7.Up", "T14.Down", "T14.Up", "muscle.Down", "muscle.Up")
  rownames(outMatrix) <- nodeSet$nodes
  outMatrix[,"GOID"] <- nodeSet$nodes
  
  for (useGO in nodeSet$nodes){
    outMatrix[useGO, "Description"] <- nodeSet$nodeData[[useGO]]$Desc
    listMems <- strsplit(nodeSet$nodeData[[useGO]]$listMembership, ",")[[1]]
    listMems <- listMems[(nchar(listMems) > 0)]
    outMatrix[useGO, listMems] <- "X"
  }
  allMems <- sapply(nodeSet$nodeData, function(x){x$listMembership})
  reOrder <- order(allMems, decreasing=TRUE)
  outMatrix <- outMatrix[reOrder,]
  print(xtable(outMatrix), type = 'html', html.table.attributes = 'style="border-spacing:20px 5px;"', include.rownames=FALSE)
  cat('\n<a href="#tableLink">back</a>\n')
}


## ----checkCollateralSprouting--------------------------------------------
allDescStrings <- sapply(smNodes, function(x){x$descStr})
isCollateral <- grep("collateral sprouting", allDescStrings, ignore.case=TRUE)

collateralGO <- smNodes[[isCollateral]]$nodes

skinRomer$T7[collateralGO,]
skinRomer$T14[collateralGO,]

rnGenes <- unique(unlist(rnGO[collateralGO]))

rnFCGenes <- rownames(skinFC$T7)
rnGenes <- rnGenes[(rnGenes %in% rnFCGenes)]
rnExtra <- cbind(unlist(mget(rnGenes, org.Rn.egSYMBOL)), unlist(mget(rnGenes, org.Rn.egGENENAME)))

rnData <- lapply(skinFC, function(inFC){
  tmp <- cbind(inFC[rnGenes,], rnExtra)
  names(tmp) <- c(names(tmp)[1:7], "Symbol", "Name")
  return(tmp)
})
lapply(rnData, dim)


## ----generateTables, echo=FALSE, results='asis'--------------------------
for (iTable in 1:length(rnData)){
  tmpData <- rnData[[iTable]]
  negEntries <- which(tmpData$logFC <= 0)
  htmlOut <- capture.output(print(xtable(tmpData), type = 'html', html.table.attributes = 'style="border-spacing:20px 5px;"', include.rownames=FALSE))
  negEntries <- negEntries + 4
  for (iNeg in negEntries){
    htmlOut[iNeg] <- sub("<TR>", '<TR style="color: red;">', htmlOut[iNeg])
  }
  
  cat('###', names(rnData)[iTable], sep=' ')
  cat('\n\n')
  cat(htmlOut, sep="\n")
  
  cat('\n')
}


## ----runGeneSetTestMuscle, eval=FALSE------------------------------------
## load("runMuscleRomer.RData")
## options(mc.cores=12) # at least if we are on hera
## t1 <- Sys.time()
## muscleGeneSetTest <- lapply(muscleFC, function(x){
##   mmGeneSetTest(muscleSet, x$t)
## })
## 
## t2 <- Sys.time()
## difftime(t2, t1)
## save(muscleGeneSetTest, t1, t2, file="inst/data/muscleGeneSetTest.RData")


## ------------------------------------------------------------------------
Sys.time()
sessionInfo()