phyloTree-class: phyloTree class

In MesKit: A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Description

S4 class for storing informations about phylogenetic tree.

Slots

patientID

patient ID.

tree

a object of class "phylo".

bootstrap.value

a numeric vector of bootstrap values.

method

approach to construct a phylogenetic tree.

binary.matrix

a presense/absent binary matrix of mutations.

ccf.matrix

a ccf matrix of mutations.

mut.branches

a data.frame of mutations per trunk/branch.

branch.type

a data.frame of trunk/branch types based on shared pattern.

ref.build

human reference genome version. Default: 'hg19'. Optional: 'hg18' or 'hg38'.

tsb.label

store relationship between Tumor_Sample_Barcode and Tumor_Sample_Label if Tumor_Sample_Label is provided in clinical data.

MesKit documentation built on March 28, 2021, 6 p.m.