missing.fun: Missing values
In MEET: MEET: Motif Elements Estimation Toolkit

Description Usage Arguments Details Author(s) See Also Examples

For each position within the matrix of aligned sequences, the probability corresponding to each nucleotide is estimated. Missing values are imputed to a multistate nucleotide with probabilities corresponding to the frequency of each nucleotide in the corresponding organism.

1	missing.fun(x, symbols, R, Prob)

`x`	Position k of the training set (a set of aligned nucleotide sequence)
`symbols`	Number of each nucleotide
`R`	Number of missing values for position
`Prob`	Probability of each base within genome

This function is included on probability function. Missing.fun has to be different NULL

Joan Maynou <joan.maynou@upc.edu>

probability

data(TranscriptionFactor)
data(BackgroundOrganism)

x<-TranscriptionFactor[,1]
resum<-table(x)
A<-resum["A"];T<-resum["T"];C<-resum["C"];G<-resum["G"];R<-resum["-"]
symbols <- c(A,T,C,G)
names(symbols) <- c("A","T","C","G")
symbols[which(is.na(symbols))] <- 0
if(is.na(R)) R <- 0
prepm<-missing.fun(x,symbols,R,Prob)