makeGphmmPerRead: Create a function to compute gphmm probabilities during the...

In gphmm: Generalized Pair Hidden Markov Chain Model for Sequence Alignment

Description

makeGphmmPerRead returns a function to compute gphmm probabilities for each row of the csv file.

Usage

makeGphmmPerRead(seqs, csv)

Arguments

seqs	- DNAStringSet with DNA sequences used for the training.
csv	- data.frame with first column = queries, second column = reference sequences, third column = qv

Examples

library(Biostrings)
seqs <- DNAStringSet(c(a='ATGC', b = 'ATGG', c = 'ATGT'))
csv <- data.frame(queries = c('a', 'b'), refs = c('c', 'c'))
makeGphmmPerRead(seqs, csv)

gphmm documentation built on Oct. 2, 2017, 5:03 p.m.