initialP: To initialize clonal frequency matrix

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

Description

To initialize clonal frequency matris P. Used in initialization step of canopy.sample.

Usage

initialP(tree,sampname,cell.line)

Arguments

tree	input tree
sampname	vector of input sample names
cell.line	default to be FALSE, TRUE if input sample is cell line (no normal cell contamination)

Value

Clonal frequency matrix P.

Author(s)

Yuchao Jiang [e-mail]

Examples

data(MDA231_tree)
data(MDA231)
sampname = colnames(MDA231$R)
initialP(MDA231_tree, sampname, cell.line = TRUE)

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
       MCP1833_bone MCP1834_lung MCP2287_bone MDA-MB-231_parental MCP3481_lung
clone1         0.00         0.00         0.00                0.00         0.00
clone2         0.28         0.35         0.50                0.40         0.30
clone3         0.36         0.33         0.23                0.35         0.42
clone4         0.36         0.32         0.27                0.25         0.28

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