% 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.

}