consensus: Determine consensus sequence

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

Function calculates consensus sequence for given alignment with a threshold of user's choice.

Usage

consensus(alignment, threshold)

Arguments

alignment	output of of read.alignment function or grouped alignment created with: align_seq_mtx2grs and alignment2matrix
threshold	minimal fraction of amino acids on the certain position in all sequences of the alignment to be taken for consensus letter on this position; number in range 0-100.

Details

If maximum fraction of any amino acid on the certain position is lower than a threshold then "*" is printed instead.

Value

A character vector of length of the aligned sequence containing consesus sequence based on the input alignment

Note

Please note that this function masks the seqinr package function consensus

Examples

data("alignment")
alignment = delete_isoforms(alignment)
threshold=80 # Set the consensus threshold
consensus_sequence=consensus(alignment, threshold)

michalstolarczyk/BALCONY documentation built on May 7, 2019, 6:08 a.m.