gphmm (version 0.99.0)

computeGphmmParam: Compute gphmm parameters from counts.

Description

computeGphmmParam returns a list with gphmm parameters.

Usage

computeGphmmParam(emiTrans)

Arguments

emiTrans

- list with emission and transition counts.

Examples

# NOT RUN {
library(Biostrings)
seqs <- DNAStringSet(c(a='ATGC', b = 'ATGG', c = 'ATGT'))
csv <- data.frame(queries = c('a', 'b'), refs = c('c', 'c'))
gphmmPerRead <- makeGphmmPerRead(seqs, csv)
parameters <- initializeGphmm()
counts <- lapply(1:nrow(csv), function(i) gphmmPerRead(i, parameters))
computeGphmmParam(counts)
# }