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Score aligned sequences against a key built from an alignment

Source: R/alignment.R
alignmentScores.Rd

Computes the tests of a keyFromAlignment() key for each sequence, for classify(). The sequences must be aligned to the same coordinates the key was built with: the same alignment columns or, for a key built with a reference, an alignment that contains that reference sequence.

Usage

alignmentScores(key, alignment, reference = NULL)

Arguments

key

A key from keyFromAlignment().

alignment

As in keyFromAlignment().

reference

Sequence to number sites by; by default the reference the key was built with, if any.

Value

A sequences x features matrix: 1 if the sequence has the state the first lead of a couplet asks for, 0 if it has another state, and NA if it has a gap or an ambiguity code there.