A modified package of EstimateClonality

EstimateClonality is an R package which uses read count and copy number information to temporally and clonally dissect SNVs, written by Nicholas McGranahan (nicholas.mcgranahan@cancer.org.uk).

https://bitbucket.org/nmcgranahan/pancancerclonality/src/master/

This version fixes some issues in the original code and makes a little optimization.

Major changes

1. The original R package is not compatible with sequenza version 3.0. Now the earlyORlate() function is compatible.
2. Added support for FACETS and CNVKIT (non ASCAT data).

Minor changes

1. Part of the code is simplified.

Usage written by the original author:

# The following an is an example script to assess the clonality of one TCGA sample, 'TCGA-BT-A42C'.

rm(list=ls())

setwd("~/Downloads/McGranahan_data/Estimate_Clonality_Package/")

install.packages("EstimateClonality_1.0.tar.gz",repos=NULL,type='source')

library("EstimateClonality")

clonality.estimation(mutation.table.loc="BLCA.mutation.table.txt" ,seg.mat.loc="tcga.blca.seg.hg19.rdata" ,data.type='TCGA_BLCA' ,TCGA.barcode="TCGA-BT-A42C" ,ANALYSIS.DIR="example2/")