Clustering of sequences based on regular expression

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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

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Arguments

ngrams

list of elements

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.

Value

List of four

  • "regExps"regular expression in best clustering

  • "seqClustering"clustering of sequences in best clustering

  • "allRegExps"all regular expressions.

  • "allIndices"all clusterings

Examples

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data(human_cleave)
#cluster_reg_exp is computationally expensive

results <- cluster_reg_exp(human_cleave[1L:10, 1L:4])

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