mapsce2r: mapsce2r

In MarkTranHS/MAPSCE: MAPping SubClonal Events

mapsce2r

Description

mapsce2r returns a matrix with a branch test for every single branch of a tree

Usage

mapsce2r(
  copy_number,
  cluster_ccf,
  tree,
  print_raw_matrix = F,
  print_duration = T,
  clone_ccf = F,
  consensus = F,
  before = 0,
  after = 0,
  print_warning = T
)

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
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.
print_raw_matrix	logical, printing of raw results
print_duration	logical, printing of the time taken to run
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
print_warning	a logical vector, option to print the warning messages

Value

a tibble with column names:

• branch. branch ID

• before. copy number state before

• after. copy number state after

• rss. residual square of sums

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

• nregions. number of regions

• nclones. number of clones or branches.

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

• bic. bic calculated from mean RSS

• bf. the strength of evidence of bayes factor comparison

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

• index. ordering of results.

Examples

data(example_data)
mapsce2r(example_cn_2r, example_ccf_2r, example_tree_2r)
#returns a tibble with branch 2 as the best result

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