getclonalcomposition: To get clonal composition

In Canopy: Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing

Description

To get clonal composition (mutational profile of each clone) of tree. Used in canopy.post.

Usage

getclonalcomposition(tree)

Arguments

tree	input tree

Value

List of each clone's mutational profile.

Author(s)

Yuchao Jiang [e-mail]

Examples

data(MDA231_tree)
getclonalcomposition(MDA231_tree)

Example output

Loading required package: ape
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-1 (2017-07-02) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps
Loading required package: pheatmap
Loading required package: scatterplot3d
[[1]]
[1] "None"

[[2]]
[1] "ALPK2"     "BRAF"      "KRAS"      "chr19_dup" "chr7_dup" 

[[3]]
[1] "ALPK2"     "BRAF"      "KRAS"      "RYR1"      "chr12_LOH" "chr12_dup"
[7] "chr19_dup" "chr7_LOH"  "chr7_dup" 

[[4]]
[1] "ALPK2"     "BRAF"      "KRAS"      "chr12_dup" "chr18_LOH" "chr19_dup"
[7] "chr7_dup" 

Canopy documentation built on May 1, 2019, 7:59 p.m.