IHC Threshold Determination

IHC Threshold Determination

Usage

ihcthreshold(
  data,
  sampleArea,
  threshold,
  positiveCells,
  negativeCells,
  totalCells = NULL,
  stainType = "ki67",
  tissueType = "other",
  optimizationMethod = "cv",
  showSummaryTable = TRUE,
  showThresholdComparison = TRUE,
  showOptimalThreshold = TRUE,
  showPlot = TRUE,
  plotType = "line",
  showMethodology = TRUE,
  showReferences = FALSE,
  confidenceLevel = 0.95,
  minSampleAreas = 5
)

Arguments

data

.

sampleArea

Identifier for each sample area examined (e.g., field1, field2, etc.). Multiple areas should be randomly selected across the tissue.

threshold

Threshold level tested (e.g., 1, 2, 3 or actual intensity values like 100, 150, 200). Multiple thresholds should be tested to find optimal discrimination.

positiveCells

Number of cells classified as positive at this threshold level.

negativeCells

Number of cells classified as negative at this threshold level.

totalCells

Total number of cells counted. If not provided, calculated as positive + negative.

stainType

Type of immunohistochemical stain being analyzed.

tissueType

.

optimizationMethod

Method for selecting optimal threshold: - CV: Choose threshold with lowest coefficient of variation across samples - Variance: Choose threshold with minimum variance in positive ratio - Consistency: Choose threshold where positive/negative ratio is most consistent

showSummaryTable

.

showThresholdComparison

Compare positive ratios across thresholds and sample areas.

showOptimalThreshold

Display detailed analysis of optimal threshold selection.

showPlot

Visualize positive ratios across thresholds and sample areas.

plotType

.

showMethodology

.

showReferences

.

confidenceLevel

.

minSampleAreas

Minimum number of sample areas needed for reliable threshold determination. Kayser et al. (2009) recommend at least 5 areas.

Value

A results object containing:

results$summaryTable					a table
results$thresholdComparison					a table
results$optimalThreshold					a table
results$plot					an image
results$methodology					a html
results$references					a html

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

results$summaryTable$asDF

as.data.frame(results$summaryTable)