--- a
+++ b/man/compMut.Rd
@@ -0,0 +1,86 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compMut.R
+\name{compMut}
+\alias{compMut}
+\title{Comparison of mutational frequency}
+\usage{
+compMut(
+  moic.res = NULL,
+  mut.matrix = NULL,
+  freq.cutoff = 0.05,
+  test.method = "fisher",
+  p.adj.method = "BH",
+  doWord = TRUE,
+  doPlot = TRUE,
+  innerclust = TRUE,
+  res.path = getwd(),
+  tab.name = NULL,
+  fig.path = getwd(),
+  fig.name = NULL,
+  annCol = NULL,
+  annColors = NULL,
+  mut.col = "#21498D",
+  bg.col = "#dcddde",
+  p.cutoff = 0.05,
+  p.adj.cutoff = 0.05,
+  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
+    "#023E8A", "#9D4EDD"),
+  width = 8,
+  height = 4
+)
+}
+\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{mut.matrix}{A binary matrix storing binary mutation data with entries of 0 and 1 only.}
+
+\item{freq.cutoff}{A numeric value to indicate the frequency cutoff for mutation data. Specifically, only features that mutated in over than such proportion would be included in testing; 0.05 by default.}
+
+\item{test.method}{A string value to indicate statistical method for independency testing. Allowed values contain c('fisher', 'chisq'); fisher by default.}
+
+\item{p.adj.method}{A string value to indicate the correction method for multiple comparision. Allowed values contain c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr'); BH by default.}
+
+\item{doWord}{A logic value to indicate if transformating the .txt outfile to a .docx WORD file (.txt file will be also kept); TRUE by default.}
+
+\item{doPlot}{A logic value to indicate if generating oncoprint; TRUE by default.}
+
+\item{innerclust}{A logic value to indicate if perform clustering within each subtype; TRUE by default.}
+
+\item{res.path}{A string value to indicate the path for saving the table.}
+
+\item{tab.name}{A string value to indicate the name of the output table.}
+
+\item{fig.path}{A string value to indicate the output path for storing the oncoprint.}
+
+\item{fig.name}{A string value to indicate the name of the oncoprint.}
+
+\item{annCol}{A data.frame storing annotation information for samples.}
+
+\item{annColors}{A list of string vectors for colors matched with annCol.}
+
+\item{mut.col}{A string vector to indicate the mutation color for oncoprint.}
+
+\item{bg.col}{A string vector to indicate the background color for oncoprint.}
+
+\item{p.cutoff}{A numeric value to indicate the nominal p value cutoff for significant mutations shown in the oncoprint; 0.05 by default.}
+
+\item{p.adj.cutoff}{A numeric value to indicate the adjusted p value cutoff for significant mutations shown in the oncoprint; 0.05 by default.}
+
+\item{clust.col}{A string vector storing colors for annotating each subtype.}
+
+\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 mutational oncoprint (.pdf) if \code{doPlot = TRUE}, a data.frame storing the difference of mutational frequency among different subtypes and a corresponding table in WORD format if \code{doWord = TRUE}.
+}
+\description{
+This function is used to compare mutational frequency among different multi-omics integerative clusters to test the independency between subtypes and mutational status. An oncoprint will be also generated with significant mutations.
+}
+\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.
+}