Magee Equation - Oncotype DX Estimator

Implements the Magee Equations (Klein et al. 2013, PMID: 23503643) for estimating Oncotype DX Recurrence Score from standard pathology variables. Provides all four published equations (Original + 3 new) with risk category classification and concordance analysis.

Usage

mageeequation(
  data,
  nuclearGrade,
  mitosis,
  erHscore,
  prHscore,
  her2Status,
  her2Positive,
  nottinghamScore = NULL,
  tumorSize = NULL,
  ki67 = NULL,
  actualRS = NULL,
  erFormat = "hscore",
  prFormat = "hscore",
  equations = "all",
  lowCutoff = 15,
  highCutoff = 26,
  showIndividual = TRUE,
  showConcordance = TRUE,
  showDistribution = TRUE
)

Arguments

data

.

nuclearGrade

.

mitosis

.

erHscore

.

prHscore

.

her2Status

.

her2Positive

.

nottinghamScore

.

tumorSize

.

ki67

.

actualRS

.

erFormat

.

prFormat

.

equations

.

lowCutoff

.

highCutoff

.

showIndividual

.

showConcordance

.

showDistribution

.

Value

A results object containing:

results$todo					a html
results$notices					a html
results$equationInfo					a html
results$summaryTable					a table
results$riskTable					a table
results$concordanceTable					a table
results$individualTable					a table
results$distributionPlot					an image
results$concordancePlot					an image

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

results$summaryTable$asDF

as.data.frame(results$summaryTable)