Seeking and Finding Clones in Copy Number and Sequencing Data.

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 created the original simulated data sets used in our paper to compare the CloneSeeker algorithm to other algorithms intended to detect clones.
2. running.R analyzes all th simulated data.
3. asswssing.R compares the infered results feomthe the algorithms to the true properties of the simulated adta.
4. clinical.R applies th CloneSeeker alorithm to CLL data.
5. cnv_survival.R tsts the associations of subclones with clinical variables in CLL.
6. ``figures.R` generates the figures in the manuscript.