Included EBSeq for downstream differential expression analysis

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

diff --git a/EBSeq/man/CheckNg.Rd b/EBSeq/man/CheckNg.Rd
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+\name{CheckNg}
+\alias{CheckNg}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+CheckNgStructure
+}
+\description{
+Provide the best polynomial fit of log variance and log mean in each Ng group. 
+}
+\usage{
+CheckNg(NewMean, NewVar,nterm, xlim, ylim)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{NewMean}{
+A list contains  
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+4 plots will be returned. The first 3 are the data and the best fit line from 
+Ng=1, Ng=2 and Ng=3 group.
+The 4th plot is the scatetr plot of all the data.  
+}
+\references{
+}
+\author{
+Ning Leng
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--   or do  help(data=index)  for the standard data sets.
+
+### Simulate Isoform Level Data
+IsoGenerate=IsoSimu(DVDconstant=NULL, DVDqt1=.97, DVDqt2=.98, Conditions=as.factor(rep(c(1,2),each=5)), NumofSample=10, NumofIso=NULL, DEIsoProp=.1, Phiconstant=NULL, Phi.qt1=.4, Phi.qt2=.6, OnlyData="Y" )
+IsoList=IsoGenerate$data
+
+# Get Vectors and Run EBSeq
+ngv=c(1,2,3,2,3,2,3,2,3)
+b3v=c(1,0,0,1,1,0,0,1,1)
+b5v=c(1,0,0,0,0,1,1,1,1)
+NgV=unlist(sapply(1:9,function(i)rep(ngv[i],dim(IsoList[[i]])[1])))
+Bias3V=unlist(sapply(1:9,function(i)rep(b3v[i],dim(IsoList[[i]])[1])))
+Bias5V=unlist(sapply(1:9,function(i)rep(b5v[i],dim(IsoList[[i]])[1])))
+
+IsoData=do.call(rbind,IsoList)
+IsoEBres=NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar(Data=IsoData, NgVector=NgV, Vect5End=Bias5V, Vect3End=Bias3V, Conditions=as.factor(rep(c(1,2),each=5)),sizeFactors=rep(1,10), maxround=5)
+
+
+# Plot
+CheckNg(IsoEBres$C1Mean, IsoEBres$C1EstVar,5, c(-1,5),c(-1,7))
+
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ Ng }