DominoEffect {DominoEffect} | R Documentation |
The function identifies individual amino acid residues, which accumulate a high fraction of the overall mutation load within a protein. After detecting mutation hotspots, the function obtains UniProt/Swiss-Prot KB functional and structural annotations for the affected protein regions and checks for the sequence agreement.
DominoEffect(mutation_dataset, gene_data, snp_data, min_n_muts = 5, MAF_thresh = 0.01, flanking_region = c(200, 300), poisson.thr = 0.01, percentage.thr = 0.15, ratio.thr = 45, approach = "percentage", write_to_file = "NO")
mutation_dataset |
Object containing a table with the mutation data (e.g. TCGA point mutations mapped to protein level). |
gene_data |
DominoData object containing information about Ensembl gene annotations: gene identifiers and regresentative transcript cDNA length. |
snp_data |
Object containing a table with information on population SNPs. |
min_n_muts |
Numeric vector defining a minimum number of mutations that need to occur at the same residue. Default: 5 |
MAF_thresh |
Numeric vector that defines Minor allele frequency threshold for considering reported mutations as population SNPs. |
flanking_region |
Numeric vector that defines size of a window around the mutation that will be considered. Up to two window sizes are allowed. |
poisson.thr |
Numeric vector that defines a treshold for the adjusted p-value. Residues with an associated p-value that is lower than the defined value are reported. Default: 0.01 |
percentage.thr |
Number defining the fraction of mutations within the window that need to fall on a single residue in order for it to be classified as a hotspot. Default: 0.15 |
ratio.thr |
Number defining a requirement that a number of mutations on a single residue should exceed what would be expected by chance given a background mutation rate in the window (i.e. the surrounding region). Default: 45 |
approach |
Option to define selection criteria to use precentage.thr or ratio.thr as criterion for finding single residue mutation clusters. Options: "both", "percentage" or "ratio". Default = "percentage" |
write_to_file |
Option if the identified and annotated hotspots should be written to a file (YES or NO). Default: NO |
Results table
Marija Buljan <buljan@imsb.biol.ethz.ch> Peter Blattmann <blattmann@imsb.biol.ethz.ch>
data("SnpData", package = "DominoEffect") data("TestData", package = "DominoEffect") data("DominoData", package = "DominoEffect") hotspot_mutations <- DominoEffect(mutation_dataset = TestData, gene_data = DominoData, snp_data = SnpData)