--- a
+++ b/man/runKappa.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runKappa.R
+\name{runKappa}
+\alias{runKappa}
+\title{Run consistency evaluation using Kappa statistic}
+\usage{
+runKappa(
+  subt1 = NULL,
+  subt2 = NULL,
+  subt1.lab = NULL,
+  subt2.lab = NULL,
+  fig.path = getwd(),
+  fig.name = "constheatmap",
+  width = 5,
+  height = 5
+)
+}
+\arguments{
+\item{subt1}{A numeric vector to indicate the first appraisement. Order should be exactly the same with subt2 for each sample.}
+
+\item{subt2}{A numeric vector to indicate the second appraisement. Order should be exactly the same with subt1 for each sample.}
+
+\item{subt1.lab}{A string value to indicate the label of the first subtype.}
+
+\item{subt2.lab}{A string value to indicate the label of the second subtype.}
+
+\item{fig.path}{A string value to indicate the output path for storing the consistency heatmap.}
+
+\item{fig.name}{A string value to indicate the name of the consistency heatmap.}
+
+\item{width}{A numeric value to indicate the width of output figure.}
+
+\item{height}{A numeric value to indicate the height of output figure.}
+}
+\value{
+A figure of consistency heatmap (.pdf).
+}
+\description{
+Calculate Kappa statistic to measure the consistency between two appraisements
+}
+\details{
+This function evaluates the consistency between two appraisements that targets to the same cohort.
+For example, the NTP-predicted subtype amd PAM-predicted subtype of external cohort, or the current subtype and predicted subtype of discovery cohort.
+Therefore, the arguments `subt1` and `subt2` can be the `clust` column of `clust.res` derived from `getMOIC()` with one specified algorithm
+or `get\%algorithm_name\%` or `getConsensusMOIC()` with a list of multiple algorithms or `runNTP()` or `runPAM()`.
+However, subtypes identified from different algorithm (i.e., `get\%algorithm_name1\%` and `get\%algorithm_name2\%`) can not be evaluated
+because the subtype 1 identified from the first algorithm may not be the same subtype 1 from the second algorithm.
+}
+\examples{
+# There is no example and please refer to vignette.
+}