EBSeqHMMTest {EBSeqHMM} | R Documentation

## Identify DE genes and classify them into their most likely path in an RNA-seq experiment with ordered conditions

### Description

Identify DE genes and classify them into their most likely path in an RNA-seq experiment with ordered conditions

### Usage

    EBSeqHMMTest(Data,
    	NgVector=NULL, Conditions, AllTran=NULL,
    	AllPi0=NULL, Terms=NULL,
    	sizeFactors, NumTranStage=c(3,2),FCV=2,
    	homo=FALSE, UpdateRd=10, PIBound=.9, UpdatePI=FALSE,
    	Print=FALSE,WithinCondR=TRUE,Qtrm=.75,QtrmCut=10,
    	PenalizeLowMed=TRUE, PenalizeLowMedQt=.1,PenalizeLowMedVal=10)

### Arguments

`Data` | input data, rows are genes and columns are samples
`NgVector` | Ng vector; NULL for gene level data
`Conditions` | A factor indicates the condition (time/spatial point) which each sample belongs to.
`AllTran` | initial values for transition matrices
`AllPi0` | initial values for starting probabilities
`Terms` | Terms
`FCV` | candidate values for expected FC. Default is 2. If user wants to search through a list of candidate FCs, he/she may define FCV as a vector. e.g. By defining FCV=seq(1.4,2,.2), the function will search over (1.4 1.6 1.8 2.0). Note that searching over a number of candidate FCs will increase the running time.
`sizeFactors` | a vector indicates library size factors
`NumTranStage` | number of states in two chains
`homo` | whether the chain is assumed to be homogenious
`UpdateRd` | max number of iteration
`UpdatePI` | whether update the mixture proportion of two chains
`PIBound` | upper bound of the mixture proportion of the two chains
`Qtrm,QtrmCut` | Transcripts with Qtrm th quantile < = QtrmCut will be removed before testing. The default value is Qtrm = 0.75 and QtrmCut=10. By default setting, transcripts that have >75% of the samples with expression less than 10 won't be tested.
`WithinCondR` | By defining WithinCondR=TRUE, estimation of r's are obtained within each condition. (WithinCondR=FALSE is not suggested here)
`Print` | Whether print the elapsed-time while running the test.
`PenalizeLowMed,PenalizeLowMedQt,PenalizeLowMedVal` | Transcripts with median quantile < = PenalizeLowMedQt will be penalized

### Details

EBSeqHMMTest() function applies EBSeqHMM model with differentexpected FC's and select the optimal FC that maximizes the log likelohood. EBSeqHMMTest() calls EBHMMNBMultiEM_2chain() function which implements the EBSeqHMM model to perform statistical analysis in an RNA-seq experiment with ordered conditions based on a fixed expected FC. EBSeqHMMTest() runs EBHMMNBMultiEM_2chain() with varying FCs (default is seq(1.4,2,.2)). And it will return the results of the model with optimal FC. Here the emission distribution of each gene is assumed to be a Beta-Negative Binomial distribution with parameters (r_g, alpha, beta) , in which alpha and beta are shared by all the genes and r_g is gene specific. If not specified, r_g, alpha and beta will be estimated using method of moments. For isoform data, we assume isoforms from the same Ig group share the same beta^Ig. alpha is shared by all the isoforms and r_gi is isoform specific. The user also needs to specify an expected FC.

### Value

Pi0Out: estimated starting probabilities of each iteration.

TranOut: estimated transition probabilities of each iteration.

Pi: estimated probability of being each chain.

Alpha, Beta: estimated alpha and beta(s).

LLSum: log likelihood of the model.

QList: estimated q's.

MgAllPP: marginal PP for all paths.

MgAllMAPChar: Most likely path based on MgAllPP.

MgAllMaxVal: Highest PP based on MgAllPP.

PPMatW: Posterior probabilities of being each of the chains.

FCLikelihood: log likelihood of each FC.

### Author(s)

Ning Leng

### Examples

    data(GeneExampleData)
    CondVector <- rep(paste("t",1:5,sep=""),each=3)
    Conditions <- factor(CondVector, levels=c("t1","t2","t3","t4","t5"))
    Sizes <- MedianNorm(GeneExampleData)
    EBSeqHMMGeneOut <- EBSeqHMMTest(Data=GeneExampleData, sizeFactors=Sizes, Conditions=Conditions,
              UpdateRd=2)

[Package EBSeqHMM version 1.24.0 Index]