schneider_conservativity {BALCONY}R Documentation

Calculate Schneider conservation metric

Description

This function facilitates the calculation of Schneider conservation metric.

Usage

schneider_conservativity(alignment, weights = NULL,pseudo_counts=F)

Arguments

alignment

Alignment data read with read.alignment function

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 without weights. Using this option with pseudo-counts will be suppressed. Default: FALSE

Value

conservation_score

A vector of length equal to the length of aligned sequences

Note

Please note that the Schneider matric formula can be found in the paper listed in "See Also" section below. 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

Author(s)

Alicja Plucennik & Michal Stolarczyk

See Also

http://onlinelibrary.wiley.com/doi/10.1002/prot.10146/abstract

Examples

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

[Package BALCONY version 0.2.10 Index]