inst/auxiliary/README.md

In CloneFinder: Finding Subclones in SNP and Sequencing Data

author: Kevin R. Coombes date: 12 October 2018 title: Auxiliary Material for CloneFinfer

Overview

This directory contains a combination of material that either (1) constructs data sets that are part of the package or (2) performs some of the analyses described in our manuscript.

Package Material

1. chlens.txt is a simple table holding the lengths In base pairs) of human chromosomes. It is based on build [UNKNOWN} and was initialy obtained from [UNKNOWN].
2. makeChlens.R is a script that reads the previous file, converts it to a useful form, and saves it in the sysdata.rda file so it can be used by the package. In particular, it is used by functions that simulate Tumor objects to create realistic segmentation data.
3. makeTestExamples.R is a script that simulates copy number and mutation data used for regression testing of the algorithms during package development.

Analyses

1. simgen.R is the script that creates all the simulated data sets used in our paper to compare the CloneFinder algorithm to other algorithms intended to detect clones.

CloneFinder documentation built on May 2, 2019, 5:01 p.m.