lichee2edge: Constructing trees from variant allele frequency using...

In ymatts/PhyC: Clustering cancer evolutional trees

Description

Constructing trees from variant allele frequency using LICHeE.

Usage

lichee2edge(licheePath = NULL, vaf, licheeParamIO = NULL,
  licheeParamFilter = NULL, licheeParamPhy = NULL)

Arguments

licheePath	Path to lichee.jar file.
vaf	Matrix of variant allele frequency. For more detail of data format, see http://viq854.github.io/lichee/
licheeparamIO	List of input/output and display options.For detail see http://viq854.github.io/lichee/. You can set the parameters of (normal,save,showNetwork,showTree).
licheeparamFilter	List of SSNV filtering and calling parameters. For detail see http://viq854.github.io/lichee/. You can set the parameters of (absent,present,maxVAFValid,minProfileSupport).
licheeparamParamPhy	List of phylogenetic network construction and tree search paramters. For detail see http://viq854.github.io/lichee/. You can set the parameters of (minClusterSize,minPrivateClusterSize,minRobustNodeSupport,maxClusterDist,completeNetwork,e,nTreeQPCheck).

Value

edgeList Rooted-constraint network of cancer lineage.

edgeLenList Edge length vector corresponding to the edgeList. The edge legnth means #addition SSNVs from parental clone.

Author(s)

Yusuke Matsui & Teppei Shimamura

ymatts/PhyC documentation built on May 4, 2019, 5:30 p.m.