compute_rates_clon_excl {GeneAccord} | R Documentation |
Compute the clonal exclusivity rates for each gene-to-clone-assignment from the collection of tree inferences.
compute_rates_clon_excl(pat_tbl)
pat_tbl |
A tibble with the information of which gene/pathway is
altered in which clone in the patient, and including this information
from the collection of trees. Can be created with with
|
Takes the gene-to-clone assignment tibble as created with
create_tbl_tree_collection
and computes for each instance
from the collection of trees the rate of clonal exclusivity. This rate
is the fraction of gene/pathway pairs that were on a different branch
in the tumor phylogeny, i.e. the fraction of pairs that was clonally
exclusive.
A vector with all rates of clonal exclusivity from all tree inferences.
Ariane L. Moore
clone_tbl <- dplyr::tibble(file_name = rep("fn1", 10), "patient_id"=rep("pat1", 10), "altered_entity"=paste0("gene", LETTERS[seq_len(10)]), "clone1"=c(0, 1, 0, 1, 0, 1, 0, 1, 1, 1), "clone2"=c(1, 0, 1, 0, 1, 1, 1, 0, 0, 1), "tree_id"=c(rep(1, 5), rep(2, 5))) compute_rates_clon_excl(clone_tbl)