getZ: To get SNA genotyping matrix Z

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

Description

To get SNA genotyping matrix Z from location of SNAs on the tree. Used in canopy.sample.

Usage

getZ(tree, sna.name)

Arguments

tree	input tree
sna.name	vector of SNA names

Value

Genotyping matrix Z.

Author(s)

Yuchao Jiang [e-mail]

Examples

data(MDA231_tree)
data(MDA231)
sna.name = rownames(MDA231$R)
getZ(MDA231_tree, sna.name)

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
      clone1 clone2 clone3 clone4
BRAF       0      1      1      1
KRAS       0      1      1      1
ALPK2      0      1      1      1
RYR1       0      0      1      0

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