excl_low_prob_strcts {BALCONY}R Documentation

Exclude low probability structural data

Description

This function facilitates the exclusion of low probability structural data from the downstream conservativity analysis, which helps to reduce the effect of non-consistent structural amino acids on the conservativity analysis of the structure of interest

Usage

excl_low_prob_strcts(structure, threshold)

Arguments

structure

A structure object generated with create_structure_seq function

threshold

The threshold for the structural data exclusion

Value

structure_matrix

A matrix of characters "S" and "N" marking on sequence the structural element; "S" - amino acid forms the analyzed structure, "N" - amino acid which does not form the structure. Number of rows of the matrix corresponds to the number of structures analyzed

structure_numbers

A vector containing the numbers of the amino acids in the sequence of interest (no gaps)

structure_probabilities

A matrix of numeric values: probabilities of corresponding to the structural information from first element of the output

Author(s)

Michal Stolarczyk & Alicja Pluciennik

See Also

create_structure_seq

Examples

data("alignment")
structure_files = c(system.file("extdata", "T1_4JNC.structure", package = "BALCONY"),
                    system.file("extdata", "T2_4JNC.structure", package = "BALCONY"),
                    system.file("extdata", "T3_4JNC.structure", package = "BALCONY")
                    )
structure_list = read_structure(structure_files)
#creating library uniprot - PDB
lib=list(c("Q84HB8","4I19","4QA9"),
        c("P34913","4JNC"),
        c("P34914","1EK2","1CR6","1EK1","1CQZ"))
pdb_name = "4JNC"
uniprot=find_seqid(pdb_name,lib)
tunnel=create_structure_seq(structure_list,uniprot,alignment)
tunnel_excluded = excl_low_prob_strcts(tunnel, 0.5)

[Package BALCONY version 0.2.10 Index]