VERSO {VERSO} | R Documentation |
Perform the inference of the maximum log-likelihood VERSO phylogenetic tree.
VERSO( D, alpha = NULL, beta = NULL, initialization = NULL, random_tree = FALSE, keep_equivalent = TRUE, check_indistinguishable = TRUE, marginalize = FALSE, num_rs = 10, num_iter = 10000, n_try_bs = 1000, num_processes = Inf, verbose = TRUE, log_file = "" )
D |
Input data for the inference reporting presence (as 1), absense (as 0) or missing information (as NA) for a set of variants. |
alpha |
False positive error rate provided as a verctor; if a vector of alpha (and beta) is provided, the inference is performed for multiple values and the solution at maximum-likelihood is returned. |
beta |
False negative error rate provided as a verctor; if a vector of beta (and alpha) is provided, the inference is performed for multiple values and the solution at maximum-likelihood is returned. |
initialization |
Binary matrix representing a perfect philogeny tree; genotypes are rows and mutations are columns. This parameter overrides "random_tree". |
random_tree |
Boolean. Shall I start MCMC search from a random tree? If FALSE (default) and initialization is NULL, search is started from a TRaIT tree (BMC Bioinformatics . 2019 Apr 25;20(1):210. doi: 10.1186/s12859-019-2795-4). |
keep_equivalent |
Boolean. Shall I return results (B and C) at equivalent likelihood with the best returned solution? |
check_indistinguishable |
Boolean. Shall I remove any indistinguishable variant from input data prior inference? |
marginalize |
Boolean. Shall I marginalize C when computing likelihood? |
num_rs |
Number of restarts during MCMC inference. |
num_iter |
Maximum number of MCMC steps to be performed during the inference. |
n_try_bs |
Number of steps without changes in likelihood of best solution after which to stop the MCMC. |
num_processes |
Number of processes to be used during parallel execution. To execute in single process mode, this parameter needs to be set to either 1, NA or NULL. |
verbose |
Boolean. Shall I print to screen information messages during the execution? |
log_file |
log file where to print outputs when using parallel. If parallel execution is disabled, this parameter is ignored. |
A list of 9 elements: B, C, phylogenetic_tree, corrected_genotypes, genotypes_prevalence, genotypes_summary, log_likelihood and error_rates. Here, B returns the maximum likelihood variants tree (inner nodes of the phylogenetic tree), C the attachment of patients to genotypes and phylogenetic_tree VERSO phylogenetic tree, including both variants tree and patients attachments to variants; corrected_genotypes is the corrected genotypes, which corrects D given VERSO phylogenetic tree, genotypes_prevalence the number of patients and observed prevalence of each genotype and genotypes_summary provide a summary of association of mutations to genotypes. In equivalent_solutions, solutions (B and C) with likelihood equivalent to the best solution are returned. Finally log_likelihood and error_rates return the likelihood of the inferred phylogenetic moldel and best values of alpha and beta as estimated by VERSO.
data(variants) set.seed(12345) inference = VERSO(D = variants, alpha = c(0.01,0.05), beta = c(0.01,0.05), check_indistinguishable = TRUE, num_rs = 5, num_iter = 100, n_try_bs = 50, num_processes = 1, verbose = FALSE)