ctree: Construct a 'ctree' clone tree with known structure.

In caravagnalab/ctree: ctree - Clone trees in cancer evolution

Construct a 'ctree' clone tree with known structure.

Description

This constructor creates an object of class ''ctree'', which represents a clone tree. The tree is created from a set of clusters computed for a patient, usually with methods that carry out tumour subclonal deconvolution routines on bulk DNA sequencing data.

To create a tree a list of drivers can be provided to be annotated to an input set of CCF clusters. There are a minimum amount of information and formatting fields that are required for tree construction to operate successfully. Please refer to the package vignette and the provided input datasets for more instructions.

Usage

ctree(
  CCF_clusters,
  drivers,
  samples,
  patient,
  M,
  score,
  annotation = paste0("Clone tree for patient ", patient)
)

Arguments

CCF_clusters	Clusters of Cancer Cell Fractions available in the data of this patient. See the package vignette to see the format in which this should be specified.
drivers	A list of driver events that should be annotated to each one of the input clusters contained in the 'CCF_clusters' parameter. See the package vignette to see the format in which this should be specified.
samples	A vector of samples names (e.g., the biopsies sequenced for this patient).
patient	A string id that represent this patient.
M	The adjacency matrix defined to connect all the nodes of this tree.
score	A scalar score that can be associated to this tree.
annotation	Any string annotation that one wants to add to this 'ctree'. This will be used by some of the plotting functions that display 'ctree' objects.

Value

An object of class "ctree" that represents this tree.

See Also

This function requires the input tree to be specified in the format of an adjacency matrix; plese see function ctrees if you need to create de novo also the adjacency matrices that fit your data.

Examples

data('ctree_input')

x = ctrees(
   ctree_input$CCF_clusters,
   ctree_input$drivers,
   ctree_input$samples,
   ctree_input$patient,
   ctree_input$sspace.cutoff,
   ctree_input$n.sampling,
   ctree_input$store.max
   )
x = x[[1]]    
   
   
# Adj matrix inside of the objects, we remove the GL
# entry that is added as fake root by ctree
M = x$adj_mat
M = M[rownames(M) != 'GL', colnames(M) != 'GL']

print(M)

# Manual construction
y = ctree(
   ctree_input$CCF_clusters,
   ctree_input$drivers,
   ctree_input$samples,
   ctree_input$patient,
   M,
   score = 123456,
   annotation = paste0("Some clone tree")
)

# The same
print(x)
print(y)

caravagnalab/ctree documentation built on May 12, 2022, 4:42 p.m.