--- a
+++ b/man/compFGA.Rd
@@ -0,0 +1,74 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/compFGA.R
+\name{compFGA}
+\alias{compFGA}
+\title{Comparison of fraction genome altered}
+\usage{
+compFGA(
+  moic.res = NULL,
+  segment = NULL,
+  iscopynumber = FALSE,
+  cnathreshold = 0.2,
+  test.method = "nonparametric",
+  barcolor = c("#008B8A", "#F2042C", "#21498D"),
+  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
+    "#023E8A", "#9D4EDD"),
+  fig.path = getwd(),
+  fig.name = NULL,
+  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{segment}{A data frame containing segmented copy number and columns must exactly include the following elements: c('sample','chrom','start','end','value'). Column of `value` should be segments value when \code{iscopynumber = FALSE} but copy-number value when \code{iscopynumber = TRUE}. Copy-number will be converted to segments by log2(copy-number/2).}
+
+\item{iscopynumber}{A logical value to indicate if the fifth column of segment input is copy-number. If segment file derived from CNV calling provides copy number instead of segment_mean value, this argument must be switched to TRUE. FALSE by default.}
+
+\item{cnathreshold}{A numeric value to indicate the cutoff for identifying copy-number gain or loss. 0.2 by default.}
+
+\item{test.method}{A string value to indicate the method for statistical testing. Allowed values contain c('nonparametric', 'parametric'); nonparametric means two-sample wilcoxon rank sum test for two subtypes and Kruskal-Wallis rank sum test for multiple subtypes; parametric means two-sample t-test when only two subtypes are identified, and anova for multiple subtypes comparison; "nonparametric" by default.}
+
+\item{barcolor}{A string vector to indicate the mapping color for bars of FGA, FGG and FGL.}
+
+\item{clust.col}{A string vector storing colors for each subtype.}
+
+\item{fig.path}{A string value to indicate the output path for storing the barplot.}
+
+\item{fig.name}{A string value to indicate the name of the barplot.}
+
+\item{width}{A numeric value to indicate the width of barplot.}
+
+\item{height}{A numeric value to indicate the height of barplot.}
+}
+\value{
+A list contains the following components:
+
+        \code{summary}           a table summarizing the measurements of FGA, FGG, and FGL per sample
+
+        \code{FGA.p.value}       a nominal p value quantifying the difference of FGA among current subtypes
+
+        \code{pairwise.FGA.test} a pairwise BH adjusted p value matrix for multiple comparisons of FGA if more than 2 subtypes were identified
+
+        \code{FGG.p.value}       a nominal p value quantifying the difference of FGG among current subtypes
+
+        \code{pairwise.FGG.test} a pairwise BH adjusted p value matrix for multiple comparisons of FGG if more than 2 subtypes were identified
+
+        \code{FGL.p.value}       a nominal p value quantifying the difference of FGL among current subtypes
+
+        \code{pairwise.FGL.test} a pairwise BH adjusted p value matrix for multiple comparisons of FGL if more than 2 subtypes were identified
+
+        \code{test.method}       a string value indicating the statistical testing method to calculate p values
+}
+\description{
+This function calculates Fraction Genome Altered (FGA), Fraction Genome Gained (FGG), and Fraction Genome Lost (FGL) seperately, and compares them among curent subtypes identified from multi-omics integrative clustering algorithms.
+}
+\examples{
+# There is no example and please refer to vignette.
+}
+\references{
+Cerami E, Gao J, Dogrusoz U, et al. (2012). The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer Discov, 2(5):401-404.
+
+Gao J, Aksoy B A, Dogrusoz U, et al. (2013). Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal, 6(269):pl1-pl1.
+}