cluster_reg_exp: Clustering of sequences based on regular expression
Description
Clusters sequences hierarchically with regular expressions.
At each step we minimize number of degrees of freedom for all regular
expressions needed to describe the data
Usage
cluster_reg_exp(ngrams)
Arguments
ngrams
list of elements
Value
List of four
"regExps"regular expression in best clustering
"seqClustering"clustering of sequences in best clustering
"allRegExps"all regular expressions.
"allIndices"all clusterings
Details
Regular expression is a list of the length equal to the length
of the input sequences. Each element of the list represents a position in
the sequence and contains amino acid, that are likely to occure on this
position.