getQ: To get SNA-CNA genotyping matrix

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

Description

To get SNA-CNA genotyping matrix Q, which specifies whether an SNA precedes a CNA. Used in canopy.sample.

Usage

getQ(tree, Y, C)

Arguments

tree	input tree
Y	SNA CNA overlapping matrix
C	CNA and CNA region overlapping matrix

Value

Genotyping matrix Q.

Author(s)

Yuchao Jiang [e-mail]

Examples

data(MDA231_tree)
data(MDA231)
Y = MDA231$Y
C = MDA231$C
getQ(MDA231_tree, Y, C)

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
      chr7_1 chr7_2 chr12_1 chr12_2 chr18 chr19
BRAF       1      1       0       0     0     0
KRAS       0      0       1       1     0     0
ALPK2      0      0       0       0     1     0
RYR1       0      0       0       0     0     0

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