BALCONY (version 0.2.10)

shannon_conservativity: Calculate Shannon conservation metric

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 withouth weights. Using these option with pseudo-counts will be suppressed. Default: FALSE

Value

conservation_score

A vector of length equal to the length of aligned sequences

See Also

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

Examples

# NOT RUN {
data("small_alignment")
# }
# NOT RUN {
conservation_score = shannon_conservativity(alignment)
# }