compare_cons_metrics: Compare conservation metrics

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

This function is designed to compare the conservation metrics used in the analysis. This way the user can notice the significant correlation or differences between these to evaluate their performance in a specific case.

Usage

compare_cons_metrics(protein_entropy, structure_profile, pdb_name)

Arguments

protein_entropy	List of entropy scores values for a whole protein (output of get_prot_entropy)
structure_profile	Each element is a list of entropy values (matrix of entropy scores) and indices of residues building structure in protein of interest (output of prepare_structure_profile)
pdb_name	The name of the analyzed protein

Details

This function allows to show the scatterplots of an entropy scores. The protein is marked as gray points, the structures are marked with symbols. It is useful to visualise differences between entropy scores, and choose the best one for further analysis.

Value

This function produces a set of scatter plots facilitating the visual inspection of entropy metrics dependancies

Examples

data("alignment")
alignment = delete_isoforms(alignment)
data("structure")
uniprot="P34913"
indices=get_structures_idx(structure)
protein_index = indices$proteinIndices
structure_index = indices$structureIndices
entropy_scores_list=list(
  Schneider_entropy = schneider_conservativity(alignment),
  Escore_entropy = Escore_conservativity(alignment)
)
structure_entropy=get_structures_entropy(structure_index, entropy_scores_list)

structure_profile = prepare_structure_profile(structure, structure_entropy)
protein_entropy=get_prot_entropy(protein_index, entropy_scores_list)
compare_cons_metrics(protein_entropy, structure_profile, "1CQZ")

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