align_seq_mtx2grs {BALCONY}R Documentation

Convert amino acid symbols to groups according to their properties of user's choice.

Description

This function performs a conversion of amino acid symbols to group symbols according to their properties. Implemented grouping methods are: substitution_matrix (majority of properties taken into account), polarity, size and aromaticity. "GX", where X stands for group number, are group symbols.

Usage

align_seq_mtx2grs(aligned_sequences_matrix,grouping_method)

Arguments

aligned_sequences_matrix

A matrix that contains aligned sequences. It is an output of alignment2matrix function

grouping_method

A string which specifies the grouping method to be used. One of following: 'substitution_matrix', 'polarity', 'size', 'aromaticity'

Value

grouped_aligned_sequences_matrix

A matrix of size of the input matrix but with group symbols instead of amino acid symbols

Author(s)

Alicja Pluciennik & Michal Stolarczyk

See Also

alignment2matrix, read.alignment

Examples

data(alignment)
alignment = delete_isoforms(alignment)
grouping_method = "general"
aligned_sequences_matrix = alignment2matrix(alignment)
grouped = align_seq_mtx2grs(aligned_sequences_matrix,grouping_method)

[Package BALCONY version 0.2.10 Index]