View source: R/ActiveDriverWGS.R
ActiveDriverWGS | R Documentation |
ActiveDriverWGS is a driver discovery tool for simple somatic mutations in cancer whole genomes
ActiveDriverWGS( mutations, elements, sites = NULL, window_size = 50000, filter_hyper_MB = 30, recovery.dir = NULL, mc.cores = 1, ref_genome = "hg19", detect_depleted_mutations = FALSE )
mutations |
A data frame containing the following columns: chr, pos1, pos2, ref, alt, patient.
|
elements |
A data frame containing the following columns: chr, start, end, id
|
sites |
A data frame containing the following columns: chr, start, end, id
|
window_size |
An integer indicating the size of the background window in base pairs that is used to establish the expected mutation rate and respective null model. The default is 50000bps |
filter_hyper_MB |
Hyper-mutated samples carry many passenger mutations and dilute the signal of true drivers.
Samples with a rate greater than |
recovery.dir |
The directory for storing recovery files. If the directory does not exist, ActiveDriverWGS will create the directory. If the parameter is unspecified, recovery files will not be saved. As an ActiveDriverWGS query for large datasets may be computationally heavy, specifying a recovery directory will recover previously computed results if a query is interrupted. |
mc.cores |
The number of cores which can be used if multiple cores are available. The default is 1. |
ref_genome |
The reference genome used on the analysis. The default option is "hg19", other options are "hg38", "mm9" and "mm10". |
detect_depleted_mutations |
if TRUE, detect elements with significantly fewer than expected mutations. FALSE by default |
A data frame containing the results of driver discovery containing the following columns: id, pp_element, element_muts_obs, element_muts_exp, element_enriched, pp_site, site_muts_obs, site_muts_exp, site_enriched, fdr_element, fdr_site
A string identifying the element of interest
The p-value of the element
The number of patients with a mutation in the element
The expected number of patients with a mutation in the element with respect to background
A boolean indicating whether the element is enriched in mutations
The p-value of the site
The number of patients with a mutation in the site
The expected number of patients with a mutation in the site with respect to element
A boolean indicating whether the site is enriched in mutations
The FDR corrected p-value of the element
The FDR corrected p-value of the site
A V indicates the presence of site mutations
data(cancer_genes) data(cll_mutations) some_genes = c("ATM", "MYD88", "NOTCH1", "SF3B1", "XPO1", "SOCS1", "CNOT3", "DDX3X", "KMT2A", "HIF1A", "APC") result = ActiveDriverWGS(mutations = cll_mutations, elements = cancer_genes[cancer_genes$id %in% some_genes,])
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