Multifocal / Primary-Metastasis Concordance

Assesses concordance of biomarkers or mutations across multiple foci of a tumour, or between paired primary and metastasis samples. Reports per-marker concordance rates, Cohen's kappa for paired (two-sample) designs, and a case-level clonality summary.

Usage

multifocalconcordance(
  data,
  caseId,
  focusId,
  markers,
  showPerMarker = TRUE,
  showKappa = TRUE,
  showCaseLevel = TRUE,
  showDiscordance = FALSE,
  showPlot = TRUE,
  showSummary = TRUE,
  showExplanation = FALSE
)

Arguments

data

.

caseId

Identifier grouping the foci / samples that belong to the same patient.

focusId

Identifier of the focus or sample within a case (e.g. primary vs metastasis, or focus 1/2/3). Used to order paired comparisons.

markers

One or more categorical biomarker / mutation status variables to assess.

showPerMarker

.

showKappa

.

showCaseLevel

.

showDiscordance

.

showPlot

.

showSummary

.

showExplanation

.

Value

A results object containing:

results$todo					a html
results$perMarkerTable					a table
results$caseLevelTable					a table
results$discordanceTable					a table
results$plot					an image
results$summary					a html
results$explanation					a html

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

results$perMarkerTable$asDF

as.data.frame(results$perMarkerTable)