missing.fun: Missing values

Description Usage Arguments Details Author(s) See Also Examples

View source: R/missing.fun.R

Description

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.

Usage

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

Arguments

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

Details

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

Author(s)

Joan Maynou <[email protected]>

See Also

probability

Examples

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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)

MEET documentation built on May 31, 2017, 4:10 a.m.