getMutations: Get Mutational Data

In QuartPAC: Identification of mutational clusters in protein quaternary structures.

Description

Reads the mutation matrices and fasta information for each protein subunit within the quaternary structure.

Usage

getMutations(mutation_files, uniprots)

Arguments

mutation_files

A list of strings where each string is the path to a mutation matrix. A mutation matrix is a matrix of 0's (no mutation) and 1's (mutation). Each column represents a specific amino acid in the protein and each row represents an individual sample (test subject, cell line, etc). If column i in row j had a 1, that would mean that the ith amino acid for person j had a nonsynonomous mutation. As the quaternary structure can be comprised of several proteins (each with their unique uniprot id), each matrix represents the protein referenced by a specific uniprot identifier.

uniprots

A list of uniprots. The list provides the uniprot id for each of the matrices described in the mutation.data parameter.

Details

The ordering in both mutation_files and uniprots must be the identical. For example, suppose that the quaternary structure is comprised of two proteins, A and B. If the first element in mutation_files points to the mutation matrix for protein A, that means that the first element of uniprots, must be a string with the uniprot id of protein A.

Value

mut_tables	A list of the mutation matrices. There should be one mutation matrix for each uniprot id in the entire assembly.
uniprots	The uniprot ids for each of the mutation matrices. The uniprot id's are shown in the same order as the mutation matrices.
aa_counts	The number of amino acids for each uniprot. This corresponds to the number of columns in the mutation matrix that is provided as input.
canonical_lengths	The length of the protein as shown in the uniprot database. The uniprot ID must be available on uniprot.org.

Note

To see examples of mutation matrices, please look in the /emphextdata folder of the package.

References

The UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 42: D191-D198 (2014).

Examples

mutation_files <- list(
					system.file("extdata","HFE_Q30201_MutationOutput.txt", package = "QuartPAC"),
          system.file("extdata","B2M_P61769_MutationOutput.txt", package = "QuartPAC")
					)
uniprots <- list("Q30201","P61769")

(mutation.data <- getMutations(mutation_files = mutation_files, uniprots = uniprots))

QuartPAC documentation built on Nov. 8, 2020, 6:58 p.m.