excl_low_prob_strcts: Exclude low probability structural data

Description Usage Arguments Value Examples

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

1

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

Examples

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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)

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