Included EBSeq for downstream differential expression analysis

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

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+\name{GeneSimu}
+\alias{GeneSimu}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+Gene Level Simulation 
+}
+\description{
+Simulate Gene level expression data from a Negative Binomial assumption. (Without outliers)
+}
+\usage{
+GeneSimu(DVDconstant = NULL, DVDqt1 = NULL, DVDqt2 = NULL, Conditions, NumofSample, NumofGene = NULL, DEGeneProp, Phiconstant = NULL, Phi.qt1 = NULL, Phi.qt2 = NULL, Meanconstant = 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. 
+If set DVDconstant=4, all the DE genes will have fold change of 4 across two condtions. 
+If this parameter is specified, the settings of DVDqt1 and DVDqt2 will be ignored. 
+}
+  \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 to generte.
+}
+  \item{NumofGene}{
+Number of genes to generate.
+}
+  \item{DEGeneProp}{
+The proportion of genes to be generated as DE. The value should be in [0, 1].
+Besides, the same proportion of genes will be generated as EE genes with outlier. 
+The genes will be generated as EE at first, then the count of one of the samples 
+(randomly selected) will be setted as its original counts multiplied by one of (4, 6, 8, 10).
+}
+  \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.
+}
+  \item{Phi.qt1, Phi.qt2}{
+If Phiconstant is not specified, the user could use a range of empirical phi's from 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{Meanconstant}{
+Wether set the mean of each gene 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. 
+}
+
+\item{NormFactor}{
+If NormFactor is NULL, each lane will be set to be with the same library size. Otherwise NormFactor should be a 
+vector with length NumofSample. 
+}
+
+}
+\details{
+For each gene, we assumed that the expression follows a Negative Binomial distribution with mean mu_g and variance mu_g * (1 + mu_g * phi_g). 
+For DE genes, we assumed that in one condition the genes are with mean mu_g * DVD.
+mu, phi and DVD could be specified by the parameter settings.
+}
+\value{
+\item{data}{
+A matrix of expression values will be generated. The rows of the matrix refer to the genes and the columns of the matrix are the samples. The genes are named "G_1", "G_2", ... The first part of the genes will be the DE ones. (The number depends on the DEGeneProp parameter.)
+}
+\item{TrueDE}{The names of the genes 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{
+IsoSimu, IsoSimuAt, GeneSimuAt
+}
+\examples{
+GeneGenerate=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, NormFactor=rep(c(.9,1.2),5),OnlyData=T)
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ simulation }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line