phil9s/cinsignaturequantification repository overview

⁠Docker image - CINSignatureQuantification

Docker container for CINSignatureQuantification⁠ - An R package to quantify signatures of chromosomal instability on absolute copy number profiles as described in Drews et al. (Nature, 2022)⁠.

⁠Licence

Non-commercial academic use only. This image bundles CINSignatureQuantification (GAP ASL v1.0). Do not use in any commercial product or service. See LICENSE files inside the image at /licenses/

The contents of this repository are copyright (c) 2022, University of Cambridge and Spanish National Cancer Research Centre (CNIO).

The contents of this repository are published and distributed under the GAP Available Source License v1.0 (ASL).

The contents of this repository are distributed in the hope that it will be useful for non-commercial academic research, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ASL for more details.

The methods implemented in the code are the subject of pending patent application GB 2114203.9.

Any commercial use of this code is prohibited.

⁠Quick start

The CINSignatureQuantification package offers two main functions: quantifyCNSignatures and clinPredictionPlatinum. It also allows you to do the signature quantification step-by-step with these functions: createCNQuant, calculateFeatures, calculateSampleByComponentMatrix, calculateActivity and clinPredictionDenovo.

⁠Quantifying signature activies

CIN signatures can be quantified using the quantifyCNSignatures() function where the primary input is a a segment table.

mySigs = quantifyCNSignatures(TCGA_478_Samples_SNP6_GOLD)

Input can be a loaded R data.frame object or file path to a segment table. There is also support to load segment tables directly from a QDNAseqCopyNumbers object generated by QDNAseq⁠. By default, the build used is hg19 and method is drews, see function documentation for additional options.

⁠Maintenance & help

For any code bugs, feature requests, or implementation errors, please open an issue. For more information on obtaining copy number profiles, please refer to the documentation of common copy number callers like ASCAT⁠ or ABSOLUTE⁠. More information on how to work with and generate copy number signatures can be obtained from: Drews et al. (Nature, 2022)⁠ or Macintyre et al. (Nature Genetics, 2018)⁠.

⁠Citation

Please cite CINSignatureQuantification as described:

citation("CINSignatureQuantification")

⁠References

• [1] Drews et al. (Nature, 2022)⁠
• [2] Macintyre et al. (Nature Genetics, 2018)⁠

⁠Authors

Philip Smith⁠ Philip.Smith 'at' cruk.cam.ac.uk