get_prot_entropy: Get MSA-based calculated entropy for chosen protein

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

This function allows to obtain vector of entropies for one complete protein sequence from MSA (gaps introduced in alignment are omitted)

Usage

get_prot_entropy(protein_index, score_list)

Arguments

protein_index	Indices of given protein aminoacids in aligned sequence
score_list	A list of entropy scores calculated for MSA

Details

This function can be used on list of entropies or list with one element for one entropy score.

Value

A list where each element is a vector of entropy values provided in entropy_scores_list

Examples

data("structure")
data("alignment")
pdb_name = "1CQZ" #A string with path to PDB file
uniprot="P43914"
chain_identifier = "B"
structure_index=get_structures_idx(structure)
entropy_scores_list=list(Schneider_entropy = schneider_conservativity(alignment),
                                   Escore_entropy = Escore_conservativity(alignment))
prot_entropy=get_prot_entropy(structure_index$proteinIndices, entropy_scores_list)

# In case of one entropy score
entropy_scores_list = list()
entropy_scores_list[[1]] = Schneider_entropy = schneider_conservativity(alignment)
prot_entropy=get_prot_entropy(structure_index$proteinIndices, entropy_scores_list)

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