ngram: Compute n-Gram Frequencies Vector

In EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Description

Computes the n-gram frequencies vector for a given protein.

Usage

ngram(prot, k = 4)

Arguments

prot	a character string corresponding to the primary structure of the protein.
k	a positive integer, between 1 and 5, indicating the k-mer of the words to be counted.

Details

The one letter code for amino acids is used (capital).

Value

A dataframe with two columns, the first one given the peptides and the second one the corresponding absolute frequency.

References

Stuart et al. Bioinformatics 2002; 18:100-108.

See Also

ngraMatrix(), ffp(), svdgram()

Examples

ngram(bovids$Bos_taurus[1], k = 3)

EnvNJ documentation built on Sept. 27, 2021, 5:07 p.m.