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infWang · Sep 28, 2020 · 3e01221 · 3e01221
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commit 3e01221
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Showing 3 changed files with 51 additions and 13 deletions.
diff --git a/R/compClinvar.R b/R/compClinvar.R
@@ -50,19 +50,51 @@ compClinvar <- function(moic.res      = NULL,
   if(!is.element(strata, colnames(dat))) {
     stop("fail to find this strata in var2comp. Consider using NULL by default.")
   }
-  stabl <- jstable::CreateTableOne2(vars = setdiff(colnames(dat), strata),
-                                    strata = strata,
-                                    data = dat,
-                                    factorVars = factorVars,
-                                    nonnormal = nonnormalVars,
-                                    exact = exactVars,
-                                    includeNA = includeNA,
-                                    showAllLevels = TRUE,
-                                    ...)
+
+  warn <- NULL
+  tryCatch(stabl <-
+             jstable::CreateTableOne2(vars = setdiff(colnames(dat), strata),
+                                     strata = strata,
+                                     data = dat,
+                                     factorVars = factorVars,
+                                     nonnormal = nonnormalVars,
+                                     exact = exactVars,
+                                     includeNA = includeNA,
+                                     showAllLevels = TRUE,
+                                     ...),
+           warning=function(w) {
+             warn <<- append(warn, conditionMessage(w))}
+           )
+  if(grepl("NA", warn, fixed = TRUE)) { # if get warning, probably due to the failure of computing exact p value in large data
+    set.seed(19991018)
+    stabl <- jstable::CreateTableOne2(vars = setdiff(colnames(dat), strata),
+                                      strata = strata,
+                                      data = dat,
+                                      factorVars = factorVars,
+                                      nonnormal = nonnormalVars,
+                                      exact = exactVars,
+                                      includeNA = includeNA,
+                                      showAllLevels = TRUE,
+                                      argsExact = list(simulate.p.value = T), # use simulated P values then
+                                      ...)
+  } else {
+    stabl <- jstable::CreateTableOne2(vars = setdiff(colnames(dat), strata),
+                                      strata = strata,
+                                      data = dat,
+                                      factorVars = factorVars,
+                                      nonnormal = nonnormalVars,
+                                      exact = exactVars,
+                                      includeNA = includeNA,
+                                      showAllLevels = TRUE,
+                                      ...)
+  }
+
+  # trim output
   comtable <- as.data.frame(stabl)
   comtable <- cbind.data.frame(var = rownames(stabl), comtable)
   rownames(comtable) <- NULL; colnames(comtable)[1] <- " "
   comtable[is.na(comtable)] <- ""
+  comtable <- comtable[,setdiff(colnames(comtable),"sig")] # remove significance
   #print(comtable)
 
   if(is.null(tab.name)) {

diff --git a/R/getClustNum.R b/R/getClustNum.R
@@ -125,7 +125,8 @@ getClustNum <- function(data        = NULL,
   par(bty="o", mgp = c(1.9,.33,0), mar=c(3.1,3.1,2.1,3.1)+.1, las=1, tcl=-.25)
   plot(NULL, NULL,
        xlim = c(min(try.N.clust),max(try.N.clust)),
-       ylim = c(min(optk1), max(optk1)),
+       #ylim = c(min(optk1), max(optk1)),
+       ylim = c(0,1),
        xlab = "Number of Multi-Omics Clusters",ylab = "")
   rect(par("usr")[1],par("usr")[3],par("usr")[2],par("usr")[4],col = "#EAE9E9",border = FALSE)
   grid(col = "white", lty = 1, lwd = 1.5)
@@ -137,7 +138,8 @@ getClustNum <- function(data        = NULL,
   par(new = TRUE, xpd = FALSE)
   plot(NULL,NULL,
        xlim = c(min(try.N.clust),max(try.N.clust)),
-       ylim = c(min(optk2$gap), max(optk2$gap)),
+       #ylim = c(min(optk2$gap), max(optk2$gap)),
+       ylim = c(0,1),
        xlab = "",ylab = "",xaxt = "n",yaxt = "n")
   points(try.N.clust, optk2$gap, pch = 19, col = ggplot2::alpha("#E51718",0.8), cex = 1.5)
   lines(try.N.clust, optk2$gap, col = "#E51718", lwd = 2, lty = 4)

diff --git a/R/pRRophetic.R b/R/pRRophetic.R
@@ -72,8 +72,8 @@ calcPhenotype <- function(trainingExprData, trainingPtype, testExprData, batchCo
 {
 
   # check if the supplied data are of the correct classes
-  if(class(testExprData) != "matrix") stop("ERROR: \"testExprData\" must be a matrix.");
-  if(class(trainingExprData) != "matrix") stop("ERROR: \"trainingExprData\" must be a matrix.");
+  if(class(testExprData)[1] != "matrix") stop("ERROR: \"testExprData\" must be a matrix.");
+  if(class(trainingExprData)[1] != "matrix") stop("ERROR: \"trainingExprData\" must be a matrix.");
   if(class(trainingPtype) != "numeric") stop("ERROR: \"trainingPtype\" must be a numeric vector.");
   if(ncol(trainingExprData) != length(trainingPtype)) stop("The training phenotype must be of the same length as the number of columns of the training expressin matrix.");
 
@@ -567,6 +567,10 @@ pRRopheticPredict <- function(testMatrix, drug, tissueType="all", batchCorrect="
 {
   cgpTrainData <- getCGPinfo(drug, tissueType, dataset) # get the IC50 and expression data for this drug/tissueType
 
+  if(!all(!duplicated(colnames(cgpTrainData$trainDataOrd)))) { # duplicated gene expression in the same cell lines
+    cgpTrainData$trainDataOrd <- cgpTrainData$trainDataOrd[,!duplicated(colnames(cgpTrainData$trainDataOrd))]
+  }
+
   predictedPtype <- calcPhenotype(cgpTrainData$trainDataOrd, cgpTrainData$ic50sOrd, testMatrix, batchCorrect=batchCorrect, powerTransformPhenotype=powerTransformPhenotype, removeLowVaryingGenes=removeLowVaryingGenes, minNumSamples=minNumSamples, selection=selection, printOutput=printOutput, removeLowVaringGenesFrom=removeLowVaringGenesFrom)
 
   return(predictedPtype)