Biomarker Response Association

Biomarker Response Association

Usage

biomarkerresponse(
  data,
  biomarker,
  response,
  responseType = "categorical",
  positiveLevel,
  plotType = "boxplot",
  showThreshold = FALSE,
  thresholdValue = "",
  thresholdMethod = "median",
  addTrendLine = FALSE,
  trendMethod = "loess",
  performTests = FALSE,
  groupVariable = NULL,
  showCorrelation = FALSE,
  logTransform = FALSE,
  outlierHandling = "highlight",
  confidenceLevel = "0.95"
)

Arguments

data

The data as a data frame.

biomarker

Continuous biomarker measurement (e.g., expression level, concentration).

response

Treatment response variable (binary, categorical, or continuous).

responseType

Type of response variable for appropriate analysis and visualization.

positiveLevel

Specify which level represents positive response (e.g., 'Responder', 'Yes', '1'). If blank, uses second level alphabetically.

plotType

Primary visualization method for biomarker-response relationship.

showThreshold

Display threshold lines for biomarker positivity/negativity.

thresholdValue

Threshold value for biomarker positivity (if known).

thresholdMethod

Method for determining biomarker threshold.

addTrendLine

Add fitted trend line for continuous responses.

trendMethod

Method for fitting trend line.

performTests

Perform appropriate statistical tests for biomarker-response association.

groupVariable

Optional grouping variable (e.g., treatment arm, disease stage).

showCorrelation

Display correlation coefficients and tests.

logTransform

Apply log transformation to biomarker values.

outlierHandling

Method for handling outlier values.

confidenceLevel

Confidence level for intervals and tests.

Value

A results object containing:

results$todo					a html
results$dataWarning					a html
results$plot					an image
results$correlation					a table
results$threshold					a table
results$groupComparison					a table
results$statisticalTests					a table
results$postHocTests					a table
results$stratifiedAnalysis					a table

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

results$correlation$asDF

as.data.frame(results$correlation)