Included EBSeq for downstream differential expression analysis

[rsem.git] / EBSeq / man / PolyFitPlot.Rd

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+\name{PolyFitPlot}
+\alias{PolyFitPlot}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+%%  ~~function to do ... ~~
+Fit the mean-var relationship using polynomial regression
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+PolyFitPlot(X, Y, nterms, xname = "Estimated Mean", yname = "Estimated Var", pdfname = "", xlim =  c(-1,5), ylim = c(-1,7), ChangeXY = F, col = "red")
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{X}{
+The first group of values want to be fitted by the polynomial regression. ( e.g Mean of the data. )
+}
+  \item{Y}{
+The second group of values want to be fitted by the polynomial regression. ( e.g. variance of the data.) The length of Y should be the same as the length of X.
+}
+  \item{nterms}{
+How many polynomial terms want to be used.
+}
+  \item{xname}{
+Name of the x axis.
+}
+  \item{yname}{
+Name of the y axis.
+}
+  \item{pdfname}{
+Name of the plot.
+}
+  \item{xlim}{
+The x limits of the plot. 
+}
+  \item{ylim}{
+The y limits of the plot.
+
+}
+  \item{ChangeXY}{
+If ChangeXY is setted to be TRUE, X will be treated as the dependent variable and Y will be treated as the independent one. Default is FALSE.
+}
+  \item{col}{
+Color of the fitted line.
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+       The PolyFitPlot function provides a smooth scatter plot of two variables and their best fitting line of polynomial regression.
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+Ning Leng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+GeneData=GeneSimu(DVDconstant=4, DVDqt1=NULL, DVDqt2=NULL, Conditions=rep(c(1,2),each=5), NumofSample=10, NumofGene=10000, DEGeneProp=.1, Phiconstant=NULL, Phi.qt1=.25, Phi.qt2=.75, Meanconstant=NULL, OnlyData="Y")
+
+EBres=NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi(Data=GeneData,NgVector=rep(1,10^4), Vect5End=rep(1,10^4), Vect3End=rep(1,10^4), Conditions=as.factor(rep(c(1,2),each=5)), maxround=5)
+
+poly=PolyFitPlot(X=EBres$MeanList[[1]], Y=EBres$PoolVar[[1]], nterms=5, xname = "mean", yname = "var", pdfname=NULL, xlim = c(0,4.5),ylim = c(-2,8), ChangeXY = F, col = "red")
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line