Processed data for "CNSistent integration and feature extraction from somatic copy number profiles".

Description

Data processed by the CNSistent tool avaiable https://bitbucket.org/schwarzlab/cnsistent This is a result of running the data processing script on the source data available in the repository or at https://zenodo.org/records/14677713. To be used through the CNSistent library, this data should be extracted into CNSistent/out/.

Repository Structure

For each dataset of TRACERx, TCGA, and PCAWG the repository contains the following:

• filled copy number segments (*_fill.tsv) using `cns fill`
• imputed copy number segments (*_imp.tsv) using `cns imp`
• aggregated copy number segments (*_[segmentation_type].tsv) using `cns aggregate`

The aggregation methods are the following:

• fixed-size segments of 10 Mb, 5 Mb, 3 Mb, 2 Mb, 1 Mb, 500 Kb, and 250 Kb size;
• Whole chromosome, chromosome arm, and cytoband-level CN segments;
• Gene-level CN values based on the ENSEMBL and COSMIC gene sets; and
• Breakpoint clustering using distance thresholdsof 1 Mb, 500 Kb, and 250 Kb.

Each file is aggregated based on the segmentation scheme in the corresponding file called `segs_[segmentation_type].bed`