Quantifies tumor budding and assigns an ITBCC (2016) grade from the number of buds counted in a hotspot. Supports a single hotspot count, multiple candidate fields (hotspot = the densest field), and area normalization to the standard 0.785 mm2 field.
Usage
tumorbudding(
data,
budCount,
caseId = NULL,
fieldArea = 0.785,
group = NULL,
survivalTime = NULL,
survivalStatus = NULL,
eventLevel,
showGrading = TRUE,
showPerCase = FALSE,
showSurvival = TRUE,
showPlot = TRUE,
showSummary = TRUE,
showExplanation = FALSE
)Arguments
- data
.
- budCount
Number of tumor buds counted. With multiple fields per case (see Case ID), the densest field is taken as the hotspot.
- caseId
Optional case identifier. When several rows share a case ID (multiple fields), the maximum bud count is used as the hotspot for that case.
- fieldArea
Area of the counted field in mm2. Counts are normalized to the ITBCC standard 0.785 mm2 field (20x objective, 0.55 mm field diameter) before grading.
- group
.
- survivalTime
.
- survivalStatus
.
- eventLevel
.
- showGrading
.
- showPerCase
.
- showSurvival
.
- showPlot
.
- showSummary
.
- showExplanation
.
Value
A results object containing:
results$todo | a html | ||||
results$gradingTable | a table | ||||
results$perCaseTable | a table | ||||
results$survivalTable | a table | ||||
results$plot | an image | ||||
results$addGradeToData | 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$gradingTable$asDF
as.data.frame(results$gradingTable)