EBTest_ext: Extented EBTest function

In EBSeqHMM: Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

Description

Extented EBTest function

Usage

EBTest_ext(Data,NgVector=NULL,Conditions,
	sizeFactors, maxround, Pool=FALSE, NumBin=1000,
	ApproxVal=10^-10, Alpha=NULL, Beta=NULL,
	PInput=NULL,RInput=NULL,PoolLower=.25,
	PoolUpper=.75,OnlyCalcR=FALSE,Print=TRUE)

Arguments

Data	Input data, rows are genes/isoforms and columns are samples. Data should come from a two condition experiment
NgVector	Ng vector; NULL for gene level data
Conditions	A factor indicates the condition (time/spatial point) which each sample belongs to. Only two levels are allowed.
sizeFactors	a vector indicates library size factors
maxround	number of iteration
Pool	While working without replicates, user could define the Pool = TRUE in the EBTest function to enable pooling.
NumBin	By defining NumBin = 1000, EBSeq will group the genes with similar means together into 1,000 bins.
PoolLower,PoolUpper	With the assumption that only subset of the genes are DE in the data set, we take genes whose FC are in the PoolLower - PoolUpper quantile of the FCs as the candidate genes (default is 25 bin, the bin-wise variance estimation is defined as the median of the cross condition variance estimations of the candidate genes within that bin. We use the cross condition variance estimations for the candidate genes and the bin-wise variance estimations of the host bin for the non-candidate genes.
ApproxVal	The variances of the transcripts with mean < var will be approximated as mean/(1-ApproxVal).
Alpha,Beta,PInput,RInput	If the parameters are known and the user doesn't want to estimate them from the data, user may specify them here.
Print	Whether print the elapsed-time while running the test.
OnlyCalcR	if OnlyCalcR=TRUE, the function will only return estimation of r's.

Details

EBSeq_ext() function is an extension of EBTest() function, which is used to calculate the conditional probability P(X_g,t | X_g,t-1). In EBSeqHMM, we assume the conditional distribution is Beta-Negative Binomial.

Value

See EBTest

Author(s)

Ning Leng

Examples

data(GeneExampleData)
Data=GeneExampleData[,1:6]
CondVector <- rep(paste("t",1:2,sep=""),each=3)
Conditions <- factor(CondVector, levels=c("t1","t2"))
Sizes <- MedianNorm(Data[1:10,])
Out <- EBTest_ext(Data=Data[1:10,], sizeFactors=Sizes, Conditions=Conditions,
         maxround=1)

Example output

Loading required package: EBSeq
Loading required package: blockmodeling
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: testthat

Attaching package: 'EBSeqHMM'

The following object is masked from 'package:EBSeq':

    f0

time 0.14 

EBSeqHMM documentation built on Nov. 8, 2020, 5:22 p.m.