CoFrEE: An Application to Estimate DNA Copy Number from Genome-wide RNA Expression Data

Abstract

ABSTRACTWe introduce CoFrEE, a simple python-based approach to extracting copy number data from expression values that works with either RNAseq or array-based expression data. CoFrEE works best in tumor cohorts that include a subset of non-tumor tissues and is applied to processed (RSEM, RPKM or TPM) expression, rather than raw data. Experiments with real public data suggest CoFrEE can provide copy number estimations comparable to existing RNAseq-based approaches, with the advantage of also being applicable to the multitude of older expression-array cohorts.