shannon_conservativity: Calculate Shannon conservation metric
In BALCONY: Better ALignment CONsensus analYsis

Description Usage Arguments Value Note Author(s) See Also Examples

This function facilitates the calculation of Shannon conservation metric.

1	shannon_conservativity(alignment, weights = NULL,pseudo_counts=F)

`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

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

1 2	data("small_alignment") conservation_score = shannon_conservativity(alignment)

Loading required package: seqinr
Loading required package: Rpdb
Loading required package: rgl

Attaching package: 'Rpdb'

The following objects are masked from 'package:base':

    norm, replicate, unsplit

Loading required package: scales

Attaching package: 'BALCONY'

The following object is masked from 'package:seqinr':

    consensus

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found