shannon_conservativity: Calculate Shannon conservation metric

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

This function facilitates the calculation of Shannon conservation metric.

Usage

shannon_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

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

References

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

Examples

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

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