computeGphmmParam: Compute gphmm parameters from counts.
In gphmm: Generalized Pair Hidden Markov Chain Model for Sequence Alignment
Description
Usage
Arguments
Examples
Description
computeGphmmParam returns a list with gphmm parameters.
Usage
1
computeGphmmParam(emiTrans)
Arguments
emiTrans
- list with emission and transition counts.
Examples
1
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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)
gphmm documentation built on Oct. 2, 2017, 5:03 p.m.
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Description Usage Arguments Examples
Description
computeGphmmParam returns a list with gphmm parameters.
Usage
1 | computeGphmmParam(emiTrans)
|
Arguments
emiTrans |
- list with emission and transition counts. |
Examples
1 2 3 4 5 6 7 | 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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