Example size reduced

TanerArslan · Mar 4, 2019 · 0b5d88f · 0b5d88f
1 parent 6333009
commit 0b5d88f
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Showing 20 changed files with 50 additions and 48 deletions.
diff --git a/R/applyThresholdToCompartment.R b/R/applyThresholdToCompartment.R
@@ -15,9 +15,9 @@
 #'
 #'c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
 #'
-#'set.seed(1)
-#'
-#'cls <- svmClassification(c.prots[1:700], df, markerProteins)
+#'set.seed(5)
+#'c.prots <- sample(c.prots, 450)
+#'cls <- svmClassification(c.prots, df, markerProteins)
 #'
 #'test.A <- cls[[1]]$svm.test.prob.out
 #'test.B <- cls[[2]]$svm.test.prob.out

diff --git a/R/applyThresholdToNeighborhood.R b/R/applyThresholdToNeighborhood.R
@@ -16,9 +16,9 @@
 #'
 #'c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
 #'
-#'set.seed(1)
-#'
-#'cls <- svmClassification(c.prots[1:700], df, markerProteins)
+#'set.seed(5)
+#'c.prots <- sample(c.prots, 450)
+#'cls <- svmClassification(c.prots, df, markerProteins)
 #'
 #'test.A <- cls[[1]]$svm.test.prob.out
 #'test.B <- cls[[2]]$svm.test.prob.out

diff --git a/R/load.data.R b/R/load.data.R
@@ -9,7 +9,7 @@
 #'@export
 #'@examples {
 #'
-#'df <- loadData(SubCellBarCode::hcc827Ctrl)
+#'df <- loadData(SubCellBarCode::hcc827Ctrl[1:10,])
 #'}
 #'@return protein.data.df
 

diff --git a/R/markerQualityControl.R b/R/markerQualityControl.R
@@ -12,7 +12,7 @@
 #'
 #'c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
 #'
-#'r.markers <- markerQualityControl(c.prots[1:10], df)
+#'r.markers <- markerQualityControl(c.prots[1:5], df)
 #'}
 #' @import ggplot2
 #' @import gridExtra

diff --git a/R/mergeCompNeigh.R b/R/mergeCompNeigh.R
@@ -14,9 +14,9 @@
 #'
 #'c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
 #'
-#'set.seed(1)
-#'
-#'cls <- svmClassification(c.prots[1:700], df, markerProteins)
+#'set.seed(5)
+#'c.prots <- sample(c.prots, 450)
+#'cls <- svmClassification(c.prots, df, markerProteins)
 #'
 #'test.A <- cls[[1]]$svm.test.prob.out
 #'test.B <- cls[[2]]$svm.test.prob.out

diff --git a/R/plotBarcode.R b/R/plotBarcode.R
@@ -13,9 +13,9 @@
 #'
 #'c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
 #'
-#'set.seed(1)
-#'
-#'cls <- svmClassification(c.prots[1:700], df, markerProteins)
+#'set.seed(5)
+#'c.prots <- sample(c.prots, 450)
+#'cls <- svmClassification(c.prots, df, markerProteins)
 #'
 #'test.A <- cls[[1]]$svm.test.prob.out
 #'test.B <- cls[[2]]$svm.test.prob.out
@@ -33,7 +33,7 @@
 #'
 #'cls.df <- mergeCls(c.cls.df, n.cls.df)
 #'
-#'proteinPlot <- plotBarcode(cls.df, "AAED1", hcc827CtrlPSMCount)
+#'proteinPlot <- plotBarcode(cls.df, "AAR2", hcc827CtrlPSMCount)
 #'}
 #'@import ggplot2
 #'@importFrom graphics plot

diff --git a/R/probabilityThresholdCompartments.R b/R/probabilityThresholdCompartments.R
@@ -13,9 +13,9 @@
 #'
 #'c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
 #'
-#'set.seed(1)
-#'
-#'cls <- svmClassification(c.prots[1:700], df, markerProteins)
+#'set.seed(5)
+#'c.prots <- sample(c.prots, 450)
+#'cls <- svmClassification(c.prots, df, markerProteins)
 #'
 #'test.A <- cls[[1]]$svm.test.prob.out
 #'test.B <- cls[[2]]$svm.test.prob.out

diff --git a/R/probabilityThresholdNeighborhood.R b/R/probabilityThresholdNeighborhood.R
@@ -12,9 +12,9 @@
 #'
 #'c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
 #'
-#'set.seed(1)
-#'
-#'cls <- svmClassification(c.prots[1:700], df, markerProteins)
+#'set.seed(5)
+#'c.prots <- sample(c.prots, 450)
+#'cls <- svmClassification(c.prots, df, markerProteins)
 #'
 #'test.A <- cls[[1]]$svm.test.prob.out
 #'test.B <- cls[[2]]$svm.test.prob.out

diff --git a/R/svmClassifier.R b/R/svmClassifier.R
@@ -13,8 +13,9 @@
 #'
 #'c.prots <- calculateCoveredProtein(rownames(df), markerProteins[,1])
 #'
-#'set.seed(1)
-#'cls <- svmClassification(c.prots[1:700], df, markerProteins)
+#'set.seed(5)
+#'c.prots <- sample(c.prots, 450)
+#'cls <- svmClassification(c.prots, df, markerProteins)
 #'
 #'}
 #'@import caret

diff --git a/R/tSNEVisualization.R b/R/tSNEVisualization.R
@@ -17,7 +17,7 @@
 #'
 #'set.seed(21)
 #'tsneMap.df <- tsneVisualization(protein.data = df,
-#'markerProteins = c.prots[1:30],
+#'markerProteins = c.prots[1:20],
 #'dims = 2, theta = c(0.4), perplexity = c(5))
 #'}
 #'

diff --git a/man/applyThresholdCompartment.Rd b/man/applyThresholdCompartment.Rd
diff --git a/man/applyThresholdNeighborhood.Rd b/man/applyThresholdNeighborhood.Rd
diff --git a/man/computeThresholdCompartment.Rd b/man/computeThresholdCompartment.Rd
diff --git a/man/computeThresholdNeighborhood.Rd b/man/computeThresholdNeighborhood.Rd
diff --git a/man/loadData.Rd b/man/loadData.Rd
diff --git a/man/markerQualityControl.Rd b/man/markerQualityControl.Rd
diff --git a/man/mergeCls.Rd b/man/mergeCls.Rd
diff --git a/man/plotBarcode.Rd b/man/plotBarcode.Rd
diff --git a/man/svmClassification.Rd b/man/svmClassification.Rd
diff --git a/man/tsneVisualization.Rd b/man/tsneVisualization.Rd