IHC Expression Analysis

Usage

ihcstats(
  data,
  markers,
  computeHScore = FALSE,
  clusterMethod = "hierarchical",
  distanceMetric = "gower",
  nClusters = 3,
  showDendrogram = FALSE,
  showHeatmap = FALSE,
  showScoreDist = FALSE,
  pcaAnalysis = FALSE,
  standardizeData = TRUE,
  showPCAPlot = FALSE,
  showClusterValidation = FALSE,
  optimalKMethod = "elbow",
  iterativeClustering = FALSE,
  linkageMethod = "average",
  showDiagnostics = FALSE,
  groupVariable = NULL,
  scoringScale = "standard",
  tumorRegionAnalysis = FALSE,
  centralRegionVar = NULL,
  invasiveRegionVar = NULL,
  prognosticClustering = FALSE,
  survivalTimeVar = NULL,
  survivalEventVar = NULL,
  differentialDiagnosis = FALSE,
  tumorTypeVar = NULL,
  antibodyOptimization = FALSE,
  calculateDiagnosticMetrics = FALSE,
  olsenVisualization = FALSE,
  clusterCutHeight = 0.5,
  sterlacciAnalysis = FALSE,
  supervisedClustering = FALSE,
  reproductibilityTesting = FALSE,
  immuneSignatureFocus = FALSE,
  tilAnalysisMode = "combined_til",
  multipleTesting = "bonferroni",
  significanceThreshold = 5.5e-05
)

Arguments

data: The data as a data frame.
markers: IHC marker variables with categorical expression scores
computeHScore: .
clusterMethod: .
distanceMetric: .
nClusters: .
showDendrogram: .
showHeatmap: .
showScoreDist: .
pcaAnalysis: .
standardizeData: .
showPCAPlot: .
showClusterValidation: .
optimalKMethod: .
iterativeClustering: .
linkageMethod: .
showDiagnostics: .
groupVariable: .
scoringScale: .
tumorRegionAnalysis: .
centralRegionVar: .
invasiveRegionVar: .
prognosticClustering: .
survivalTimeVar: .
survivalEventVar: .
differentialDiagnosis: .
tumorTypeVar: .
antibodyOptimization: .
calculateDiagnosticMetrics: .
olsenVisualization: .
clusterCutHeight: .
sterlacciAnalysis: .
supervisedClustering: .
reproductibilityTesting: .
immuneSignatureFocus: .
tilAnalysisMode: .
multipleTesting: .
significanceThreshold: .

Value

A results object containing:

`results$todo`					a html
`results$hscoreTable`					a table
`results$clusterSummary`					a table
`results$pcaTable`					a table
`results$silhouetteTable`					a table
`results$diagnosticTable`					a table
`results$optimalMarkersTable`					a table
`results$regionalTable`					a table
`results$prognosticTable`					a table
`results$survivalTable`					a table
`results$differentialTable`					a table
`results$antibodyPerformanceTable`					a table
`results$optimalPanelTable`					a table
`results$sterlacciTable`					a table
`results$reproductibilityTable`					a table
`results$supervisedResultsTable`					a table
`results$tilSignatureTable`					a table
`results$dendrogramPlot`					an image
`results$heatmapPlot`					an image
`results$pcaPlot`					an image
`results$validationPlot`					an image
`results$scoreDist`					an image

Tables can be converted to data frames with asDF or as.data.frame. For example:

results$hscoreTable$asDF

as.data.frame(results$hscoreTable)