Description Usage Arguments Details Value Author(s) Examples
View source: R/EBHMMNBfunForMulti.R
Baum-Welch algorithm for multiple hidden markov chains
1 2 3 4 5 6 7 8 | EBHMMNBfunForMulti(Data,PPIn,
NgVector=NULL,Conditions, sizeFactors,
PriorFC=1.5,homo=TRUE, maxround=5,
Pi0=NULL, Tran=NULL, NumTranStage=3,
FCParam=NULL, AlphaIn=NULL,BetaIn=NULL,
StateNames=c("Up","NC","Down"),
EM=TRUE, UpdateParam=TRUE, Print=TRUE,WithinCondR=TRUE,
PenalizeLowMed=TRUE, PenalizeLowMedQt=.2,PenalizeLowMedVal=10)
|
Data |
input data, rows are genes/isoforms and columns are samples |
PPIn |
PPDE for all adjacent comparisons |
NgVector |
Ng vector; NULL for gene level data |
Conditions |
A factor indicates the condition (time/spatial point) which each sample belongs to. |
sizeFactors |
a vector indicates library size factors |
Tran |
initial values for transition matrices |
Pi0 |
initial values for starting probabilities |
NumTranStage |
number of states in two chains |
PriorFC |
target FC for gridient change |
StateNames |
name of the hidden states |
homo |
whether the chain is assumed to be homogenious |
maxround |
max number of iteration |
AlphaIn,BetaIn |
If the parameters are known and the user doesn't want to estimate them from the data, user may specify them here. |
FCParam |
not in use |
EM |
Whether estimate the prior parameters of the beta distribution by EM |
UpdateParam |
Whether update starting probabilities and transition probabilities |
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 |
EBHMMNBfunForMulti() function implements the Balm-Welch algorithm that estimates the starting probabilities and transition probabilities of a hidden Markov model with multiple chains. 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.
MAPTerm: the most likely path of each gene/isoform.
MAPTermNum: numeric version of MAPTerm.
AllTerm: all possible expression paths considered in the model.
PP: posterior probability of being each expression path.
WhichMax: index of the most likely path.
Allf: prior probability of being each path.
Pi0Track: estimated starting probabilities of each iteration.
TranTrack: estimated transition probabilities of each iteration.
AlphaTrack, BetaTrack: estimated alpha and beta(s).
LLAll=PostSumForLL.Sum: log likelihood of the model.
Ning Leng
1 2 3 4 5 6 | data(GeneExampleData)
CondVector <- rep(paste("t",1:5,sep=""),each=3)
Conditions <- factor(CondVector, levels=c("t1","t2","t3","t4","t5"))
Sizes <- MedianNorm(GeneExampleData)
tmp <- EBHMMNBfunForMulti(Data=GeneExampleData, PPIn=matrix(1,ncol=15, nrow=100),sizeFactors=Sizes, Conditions=Conditions,
maxround=2)
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