kolmogorov_smirnov_test: Perform Kolmogorov-Smirnov test for structural data

In BALCONY: Better ALignment CONsensus analYsis

Description

This function facilitates the comparison of conservativity of structure of interest with the rest of the protein. For example comparison of tunnel conservativity with overall protein conservativity.

Usage

kolmogorov_smirnov_test(protein_entropy, structure_entropy, alternative,
                        pdb_name = "Reference", range = NULL, make_plot = NULL)

Arguments

protein_entropy	A list of calculated entropy scores (vectors of numeric values). The output of get_prot_entropy function
structure_entropy	A list where each element is a list of structure indices in the protein and matrix with corresponding entropy values (each row is a separate score metric)
alternative	A numeric value indicating the character of alternative hypothesis of the test to be performed: 1 - two sided test, 2 - less, 3 - greater, following the generic ks.test function.
pdb_name	(optional) A string with name of the reference protein, default: "Reference"
range	(optional) A numeric vector with region of reference protein to be excluded from the data set. Useful when protein consists of additional chains with outstandingly low/high entropy values which may distort result of the test, default: NULL
make_plot	(optional) A logical indicating if cumulative distribution functions should be displayed, default: TRUE

Value

A matrix of p-values for each entropy metric (rows) and structure (columns)

Author(s)

Michal Stolarczyk & Alicja Pluciennik

See Also

ecdf, ks.test

Examples

data("alignment")
data("structure")
entropy_data=list(Schneider.entropy=schneider_conservativity(alignment),
              Escore.entropy = Escore_conservativity(alignment),
              Kabat.entropy =  kabat_conservativity(alignment))
indices=get_structures_idx(structure)
protein_index = indices$proteinIndices
structure_index = indices$structureIndices
prot_cons=get_prot_entropy(protein_index,entropy_data)
stru_entropy=get_structures_entropy(structure_index,entropy_data)
profiles_for_structure=prepare_structure_profile(structure, stru_entropy)
EQUAL=kolmogorov_smirnov_test(protein_entropy = prot_cons,
                              structure_entropy = profiles_for_structure,
                              alternative = 1,range = c(1:233),make_plot = TRUE)

BALCONY documentation built on May 1, 2019, 10:31 p.m.