landgraf_conservativity: Calculate Landgraf conservation score
In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description Usage Arguments Value Note References Examples

This function calculates Landgraf conservarion score

1	landgraf_conservativity(matrix_name = NULL, alignment, weights)

`matrix_name`	A string with path to the file woith substitution matrix to be used to calculate the Landgraf conservation score. Optional parameter, if not provided the Gonnet substitution matrix is used (according to author's suggestion)
`alignment`	An alignment object read with `read.alignment` function
`weights`	A vector with weight for each sequence in the alignment to be used to calculate the Landgraf conservation score e.g. each sequence similarity to the consensus sequence from the alignment - output from `cons2seqs_ident` fuction

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

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

data("small_alignment")
alignment = small_alignment
threshold_consensus = 30
consensus_seq=consensus(alignment, threshold_consensus);
consensus_sequences_identity=cons2seqs_ident(alignment, consensus_seq)
score = landgraf_conservativity(alignment = alignment, weights = consensus_sequences_identity)