calculate_AA_variation: Calculate AA variations on each position of the multiple sequence alignment

Description

This function calculates AA variations on each position of the alignment which may be further used for the conservativity study of the set of sequences in quiestion

Usage

calculate_AA_variation(alignment, threshold, grouped,
  grouping_method, weights, pseudo_counts=F)

Arguments

alignment

The data loaded with read.alignment function

threshold

(optional) A number in range 0-1. A of minimal frequency of occurences of amino acids at each position. Default: all the residues are visualized.

grouped

(optional) A logical indicating if the grouping of amino acids should be applied. Default: FALSE

grouping_method

(optional) A string which specifies the grouping method to be used. One of following: 'substitution_matrix', 'polarity', 'size', 'aromaticity'. Default: 'substitution_matrix'. Default: 'substitution_matrix' if grouped is TRUE.

weights

(optional) A vector of length equal number of sequences in the alignment object with weights to overcome the taxonomic bias in the conservation analysis.

pseudo_counts

(optional) A logical indicating if pseudo-counts should be added to the MSA. Pseudo-counts can be used only in non-group mode and without weights. Using these options with pseudo-counts will be suppressed. Default: FALSE

Value

Returns list of thre matrices with tabelarized symbols of the most common AA in alignment column, percentage values for contributed AA and combined one.

var_aa$AA

A matrix of AA on all alignment positions with decreasing frequencies in columns

var_aa$per

The percentage of AA frequencies corresponding to the $AA

var_aa$matrix

A combination of this two. The best suited element for visual inspection of the variability at each position

Details

The output consists of amino acids and their fractions on each position of alignment. Amino acids with occurence frequencies lower than the threshold of user's choice are excluded.

Examples

Run this code

# NOT RUN {
data("small_alignment")
alignment = delete_isoforms(small_alignment)
threshold=10
grouped = FALSE
var_aa=calculate_AA_variation(small_alignment, threshold, grouped)
# }