--- a
+++ b/man/runMarker.Rd
@@ -0,0 +1,106 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/runMarker.R
+\name{runMarker}
+\alias{runMarker}
+\title{Run identification of unique biomarkers}
+\usage{
+runMarker(
+  moic.res = NULL,
+  dea.method = c("deseq2", "edger", "limma"),
+  prefix = NULL,
+  dat.path = getwd(),
+  res.path = getwd(),
+  p.cutoff = 0.05,
+  p.adj.cutoff = 0.05,
+  dirct = "up",
+  n.marker = 200,
+  doplot = TRUE,
+  norm.expr = NULL,
+  annCol = NULL,
+  annColors = NULL,
+  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
+    "#023E8A", "#9D4EDD"),
+  halfwidth = 3,
+  centerFlag = TRUE,
+  scaleFlag = TRUE,
+  show_rownames = FALSE,
+  show_colnames = FALSE,
+  color = c("#5bc0eb", "black", "#ECE700"),
+  fig.path = getwd(),
+  fig.name = NULL,
+  width = 8,
+  height = 8,
+  ...
+)
+}
+\arguments{
+\item{moic.res}{An object returned by `getMOIC()` with one specified algorithm or `get\%algorithm_name\%` or `getConsensusMOIC()` with a list of multiple algorithms.}
+
+\item{dea.method}{A string value to indicate the algorithm for differential expression analysis. Allowed value contains c('deseq2', 'edger', 'limma').}
+
+\item{prefix}{A string value to indicate the prefix of differential expression file (use for searching files).}
+
+\item{dat.path}{A string value to indicate the path for saving the files of differential expression analysis.}
+
+\item{res.path}{A string value to indicate the path for saving the results for identifying subtype-specific markers.}
+
+\item{p.cutoff}{A numeric value to indicate the nominal p value for identifying significant markers; pvalue < 0.05 by default.}
+
+\item{p.adj.cutoff}{A numeric value to indicate the adjusted p value for identifying significant markers; padj < 0.05 by default.}
+
+\item{dirct}{A string value to indicate the direction of identifying significant marker. Allowed values contain c('up', 'down'); `up` means up-regulated marker, and `down` means down-regulated marker.}
+
+\item{n.marker}{A integer value to indicate how many top markers sorted by log2fc should be identified for each subtype; 200 by default.}
+
+\item{doplot}{A logic value to indicate if generating heatmap by using subtype-specific markers. TRUE by default.}
+
+\item{norm.expr}{A matrix of normalized expression data with rows for genes and columns for samples; FPKM or TPM without log2 transformation is recommended.}
+
+\item{annCol}{A data.frame storing annotation information for samples.}
+
+\item{annColors}{A list of string vectors for colors matched with annCol.}
+
+\item{clust.col}{A string vector storing colors for annotating each subtype at the top of heatmap.}
+
+\item{halfwidth}{A numeric vector to assign marginal cutoff for truncating values in data; 3 by default.}
+
+\item{centerFlag}{A logical vector to indicate if expression data should be centered; TRUE by default.}
+
+\item{scaleFlag}{A logical vector to indicate if expression data should be scaled; TRUE by default.}
+
+\item{show_rownames}{A logic value to indicate if showing rownames (feature names) in heatmap; FALSE by default.}
+
+\item{show_colnames}{A logic value to indicate if showing colnames (sample ID) in heatmap; FALSE by default.}
+
+\item{color}{A string vector storing colors for heatmap.}
+
+\item{fig.path}{A string value to indicate the output path for storing the marker heatmap.}
+
+\item{fig.name}{A string value to indicate the name of the marker 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.}
+
+\item{...}{Additional parameters pass to \link[ComplexHeatmap]{pheatmap}.}
+}
+\value{
+A figure of subtype-specific marker heatmap (.pdf) if \code{doPlot = TRUE} and a list with the following components:
+
+        \code{unqlist}   a string vector storing the unique marker across all subtypes.
+
+        \code{templates} a data.frame storing the the template information for nearest template prediction, which is used for verification in external cohort.
+
+        \code{dirct}     a string value indicating the direction for identifying subtype-specific markers.
+
+        \code{heatmap}   a complexheatmap object.
+}
+\description{
+This function aims to identify uniquely and significantly expressed (overexpressed or downexpressed) biomarkers for each subtype identified by multi-omics integrative clustering algorithms. Top markers will be chosen to generate a template so as to run nearest template prediction for subtype verification.
+}
+\examples{
+# There is no example and please refer to vignette.
+}
+\references{
+Gu Z, Eils R, Schlesner M (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics, 32(18):2847-2849.
+}