Description Usage Arguments Value Author(s) See Also Examples
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
1 | excl_low_prob_strcts(structure, threshold)
|
structure |
A structure object generated with |
threshold |
The threshold for the structural data exclusion |
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 |
Michal Stolarczyk & Alicja Pluciennik
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
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