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+++ b/man/runNTP.Rd
@@ -0,0 +1,67 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runNTP.R
+\name{runNTP}
+\alias{runNTP}
+\title{Run nearest template prediction}
+\usage{
+runNTP(
+  expr = NULL,
+  templates = NULL,
+  scaleFlag = TRUE,
+  centerFlag = TRUE,
+  nPerm = 1000,
+  distance = "cosine",
+  seed = 123456,
+  verbose = TRUE,
+  doPlot = FALSE,
+  fig.path = getwd(),
+  fig.name = "ntpheatmap",
+  width = 5,
+  height = 5
+)
+}
+\arguments{
+\item{expr}{A numeric matrix with row features and sample columns; data is recommended to be z-scored.}
+
+\item{templates}{A data frame with at least two columns; class (coerced to factor) and probe (coerced to character).}
+
+\item{scaleFlag}{A logic value to indicate if the expression data should be further scaled. TRUE by default.}
+
+\item{centerFlag}{A logic value to indicate if the expression data should be further centered. TRUE by default.}
+
+\item{nPerm}{An integer value to indicate the permutations for p-value estimation.}
+
+\item{distance}{A string value to indicate the distance measurement. Allowed values contain c('cosine', 'pearson', 'spearman', 'kendall'); "cosine" by default.}
+
+\item{seed}{An integer value for p-value reproducibility.}
+
+\item{verbose}{A logic value to indicate whether console messages are to be displayed; TRUE by default.}
+
+\item{doPlot}{A logic value to indicate whether to produce prediction heatmap; FALSE by default.}
+
+\item{fig.path}{A string value to indicate the output path for storing the nearest template prediction heatmap.}
+
+\item{fig.name}{A string value to indicate the name of the nearest template prediction 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 predictive heatmap by NTP (.pdf) and a list with the following components:
+
+        \code{ntp.res}    a data.frame storing the results of nearest template prediction (see \link[CMScaller]{ntp}).
+
+        \code{clust.res}  similar to `clust.res` returned by `getMOIC()` or `get%algorithm_name%` or `getConsensusMOIC()`.
+
+        \code{mo.method}  a string value indicating the method used for prediction.
+}
+\description{
+Using Nearest Template Prediction (NTP) based on predefined templates derived from current identified subtypes to assign potential subtype label on external cohort.
+}
+\examples{
+# There is no example and please refer to vignette.
+}
+\references{
+Hoshida, Y. (2010). Nearest Template Prediction: A Single-Sample-Based Flexible Class Prediction with Confidence Assessment. PLoS ONE 5, e15543.
+}