Analyses circulating-tumour-DNA (ctDNA) / minimal-residual-disease (MRD) kinetics from paired baseline and follow-up variant allele fractions (VAF): clearance vs persistence classification, log-fold change, and MRD status as a predictor of survival by a landmark analysis.
Usage
ctdnadynamics(
data,
baselineVaf,
followupVaf,
detectionThreshold = 0.05,
timeBetween = NULL,
group = NULL,
survivalTime = NULL,
survivalStatus = NULL,
eventLevel,
conf_level = 0.95,
showClassification = TRUE,
showDynamics = TRUE,
showSurvival = TRUE,
showPlot = TRUE,
showSummary = TRUE,
showExplanation = FALSE
)Arguments
- data
.
- baselineVaf
Variant allele fraction (or ctDNA concentration) at baseline / pre-treatment.
- followupVaf
Variant allele fraction (or ctDNA concentration) at the follow-up / MRD timepoint.
- detectionThreshold
VAF at or below which the follow-up sample is classed as cleared / MRD-negative.
- timeBetween
Time between the baseline and follow-up draws, used to report a clearance rate (change in log VAF per unit time).
- group
Optional grouping variable (e.g. treatment arm) for stratified clearance rates.
- survivalTime
.
- survivalStatus
.
- eventLevel
.
- conf_level
.
- showClassification
.
- showDynamics
.
- showSurvival
.
- showPlot
.
- showSummary
.
- showExplanation
.
Value
A results object containing:
results$todo | a html | ||||
results$classificationTable | a table | ||||
results$dynamicsTable | a table | ||||
results$survivalTable | a table | ||||
results$plot | an image | ||||
results$addStatusToData | an output | ||||
results$summary | a html | ||||
results$explanation | a html |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$classificationTable$asDF
as.data.frame(results$classificationTable)