initialP: To initialize clonal frequency matrix

Description Usage Arguments Value Author(s) Examples

View source: R/initialP.R

Description

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

Usage

1
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 [email protected]

Examples

1
2
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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 Dec. 23, 2017, 5:09 p.m.