Escore_conservativity: Calculate the Escore conservation metric

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

This function facilitates the calculation of Escore conservation metric (in amino acid or group mode)

Usage

Escore_conservativity(alignment, grouping_method = NULL,
  weights = NULL, pseudo_counts = F)

Arguments

alignment	data read with read.alignment function
grouping_method	(optional) A string which specifies the grouping method to be used. One of following: 'substitution_matrix', 'polarity', 'size', 'aromaticity', default: NULL
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

Details

The conservativity score is calculated according to the following formula:

P(i) = max(p(i))/n(i)

Pnorm(i) = P(i)/max(P)

score = -ln(P_norm(i))/max(-ln(P_norm))

where:
p(i) - amino acids frequency on i-th position where gaps are included
n(i) - amino acids count on i-th position where gaps are excluded

Value

A vector of length equal to the length of aligned sequences

Note

Also, this function originally calculates the entropy values which can be used to estimate the conservativity score according to the following formula:

conservation = 1 - entropy

Examples

data("small_alignment")
conservation_score = Escore_conservativity(alignment)

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