cons2seqs_ident {BALCONY}R Documentation

Identity of each sequence in the alignment to the consensus sequence.

Description

The function calculates identity of consensus to each sequence in the alignment. It facilitates an assessment of consensus accuracy and identification of outlying sequences in the alignment. Also, it can be used to weight conservativity metrics results in further steps of analysis with BALCONY package.

Usage

cons2seqs_ident(alignment, consensus_seq)

Arguments

alignment

Data loaded with read.alignment function

consensus_seq

Consensus sequence (output of consensus function)

Details

Returned values are percentage of identical symbols (AA and "-") in consensus sequence and aligned sequence.

Value

percentage

Numeric vector of identity score (percentage); positions in the numeric vector correspond to sequences in alignment, respectively

Author(s)

Alicja Pluciennik & Michal Stolarczyk

See Also

consensus cons2seqs_sim

Examples

data("alignment")
alignment = delete_isoforms(alignment)
threshold=60
consensus=consensus(alignment, threshold)
true_consensus=cons2seqs_ident(alignment, consensus)


[Package BALCONY version 0.2.10 Index]