changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

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

diff --git a/EBSeq/man/PolyFitPlot.Rd b/EBSeq/man/PolyFitPlot.Rd
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--- a/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