shannon_conservativity {BALCONY} | R Documentation |
This function facilitates the calculation of Shannon conservation metric.
shannon_conservativity(alignment, weights = NULL,pseudo_counts=F)
alignment |
Alignment data read with |
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 |
conservation_score |
A vector of length equal to the length of aligned sequences |
Please note that the Shannon 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
Alicja Plucennik & Michal Stolarczyk
http://onlinelibrary.wiley.com/doi/10.1002/prot.10146/abstract
data("small_alignment") conservation_score = shannon_conservativity(alignment)