Included EBSeq for downstream differential expression analysis

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

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+\name{IsoSimu}
+\alias{IsoSimu}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+Isoform level simulation
+}
+\description{
+Simulate isoform level expression data from a Negative Binomial assumption. (Without outliers)
+}
+\usage{
+IsoSimu(DVDconstant = NULL, DVDqt1 = NULL, DVDqt2 = NULL, Conditions, NumofSample, NumofIso = NULL, DEIsoProp, Phiconstant = NULL, Phi.qt1 = NULL, Phi.qt2 = NULL, NormFactor = NULL, OnlyData = T)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{DVDconstant}{
+Whether want to use constant fold change value for all the DE genes.
+}
+  \item{DVDqt1, DVDqt2}{
+If DVDconstant is not specified, the user could use a range of empirical DVD's f
+rom Gould' data. The lower and upper bound ( quantile) could be specified.
+The suggested value is c(.96, .97). DVD for each gene will be randomly choosed within the range.
+}
+  \item{Conditions}{
+A vector of charecters to show each sample's condition.
+(Only the two-condition case is supported now)
+}
+  \item{NumofSample}{
+Number of samples the user want to generate.
+}
+  \item{NumofIso}{
+Input should be a vector with length 3. All values should be non-negative.
+The ith value represents how many isoforms the user want to generate for isoform group i. 
+}
+  \item{DEIsoProp}{
+The proportion of isoforms to be generated as DE. The value should be in [0, 1].
+}
+  \item{Phiconstant}{
+Whether set the disperse parameter phi to be a constant. If this parameter is specified, the settings of Phi.qt1 and Phi.qt2 will be ignored.
+Input should be a vector with length 3. The ith value indicates the overdisperse parameter of isoform group i.
+}
+  \item{Phi.qt1, Phi.qt2}{
+If Phiconstant is not specified, the user could use a range of empirical phi's from each group of Gould' data. The lower and upper bound ( quantile) could be specified.
+The suggested value is c(.25, .75). phi for each gene will be randomly choosed w
+ithin the range.
+
+}
+  \item{NormFactor}{
+Wether set the mean of each isoform to be a constant.
+}
+  \item{OnlyData}{
+Wether the user only want the generated data matrix. If OnlyData = T, the function will return the simulated matrix
+and the name of the DE genes.
+Otherwise the funtion will run DESeq, EBSeq, edgeR, baySeq and BBSeq and provide the results of each method.
+Currently only OnlyData=T is supported
+}
+}
+\details{
+For each isoform, we assumed that the expression follows a Negative Binomial distribution with mean mu_gi and variance mu_gi * (1 + mu_gi * phi_gi).
+For DE genes, we assumed that in one condition the genes are with mean mu_gi * DVD.
+mu, phi and DVD could be specified by the parameter settings.
+
+}
+\value{
+\item{data}{
+A list of expression values will be generated. 
+Each list represents a group of isoforms.
+Group1: Ng1
+Group2: Ng2
+Group3: Ng3
+The rows refer to the isoforms and the columns are the samples. 
+The isoforms are named "I_GroupNumber_IsoformNumber". The first part of the isoforms of each group will be the DE ones. (The number depends on the DEIsoProp parameter.)
+}
+\item{TrueDE}{The names of the isoforms who are defined to be DE.}
+
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+Ning Leng
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+GeneSimu
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--   or do  help(data=index)  for the standard data sets.
+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=.25, Phi.qt2=.75, OnlyData=T )
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line