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

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

diff --git a/EBSeq/man/CheckNg.Rd b/EBSeq/man/CheckNg.Rd
deleted file mode 100644 (file)
index 9571d03..0000000
--- a/EBSeq/man/CheckNg.Rd
+++ /dev/null
@@ -1,66 +0,0 @@
-\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 }