mapsce: mapsce

In MarkTranHS/MAPSCE: MAPping SubClonal Events

mapsce

Description

mapsce returns a matrix with a branch test for every single branch of a tree

Usage

mapsce(
  copy_number,
  cluster_ccf,
  mutation_ccf,
  tree,
  bootstraps = 100,
  print_raw_matrix = F,
  print_duration = T,
  print_mapsce2r = T,
  force_bootstrap = F,
  force_mapsce2r = F,
  clone_ccf = F,
  consensus = F,
  before = 0,
  after = 0
)

Arguments

copy_number	a numeric vector with copy number values ordered by sample
cluster_ccf	a matrix with mean CCF values for clones in rows and samples (same order as in copy_number) in columns
mutation_ccf	a tibble or data frame where the first columns contain the mutational CCF values for the samples (same order as in copy_number) in columns. Tw of the columns in this object need to be "PycloneCluster" and "CleanCluster", the former being the clone assignment and the latter being the PyClone filter (1 for valid clusters, 0 for clusters to be ignored)
tree	a matrix listing all the branches in the tree, where the first column is the ancestral node and the second column is the descendant clone. By definition, the root node will only be present in the first column. The clone IDs must correspond to the cluster IDs in cluster_ccf and mutation_ccf.
bootstraps	number of bootstraps for reclustering of the CCF
print_raw_matrix	logical, printing of raw results
print_duration	logical, printing of the time taken to run
print_mapsce2r	logical, printing whether mapsce is running mapsce2r
force_bootstrap	logical, forcing mapsce to run bootstrapping for patients with 2 regions only
force_mapsce2r	logical, forcing mapsce to always run mapsce2r without bootstraping, regardless of number of regions
clone_ccf	logical, forcing mapsce to use clone CCF instead of just cluster CCF
consensus	logical, forcing mapsce to run the get_consensus function
before	a numeric vector, forcing a CN before
after	a numeric vector, forcing a CN after

Value

a tibble with column names:

• branch. branch ID

• before. copy number state before

• after. copy number state after

• rss. average residual square of sums of all bootstraps

• btn. how many bootstrapped BICs are better than the null's BIC

• nregions. number of regions

• nclones. number of clones or branches.

• null. whether the branch is a trunk or not.

• bic. average bic for all bootstraps calculated from mean RSS

• bf. the strength of good_resultence of bayes factor comparison

• good_result. 1 for good results based on the Bayes Factor comparison and btn

• index. ordering of results.

Examples

data(example_data)
mapsce(example_cn, example_ccf, example_mutational_ccf, example_tree)
#returns a tibble with branch 7 as the best result

MarkTranHS/MAPSCE documentation built on Jan. 28, 2024, 6:29 p.m.