HMMcopy example dataset

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Description

A set of data of chromosome 6 of matched tumour normal pair. The dataset that is described here belongs to a female triple-negative breast cancer patient from the dataset published in Shah2012,Ha2012. This genome library was sequenced on the ABI/Life SOLiD platform, generating hybrid lengths of 25bp and 50bp paired-end reads. The reads were aligned using BioScope https://products.appliedbiosystems.com/ where reads mapped to multiple sites were ignored.

tumour_reads

The number of short reads in fixed width windows across the chromosome, generated with wigsToRangedData from WIG files

tumour_copy

Tumour copy number profile generated by correcting ‘tumour_reads’ with correctReadcount

normal_copy

Normal copy number profile generated via correctReadcount

tumour_param

Parameters for segmenting ‘tumour_copy’ in HMMsegment

tumour_segments

Segmented output of ‘tumour_copy’ HMMsegment

using ‘tumour_param’

Usage

1

Format

‘tumour_reads’, ‘tumour_copy’, and ‘normal_copy’ are RangedData objects.

‘tumour_param’ is a numeric matrix.

‘tumour_segments’ is a list.

References

Gavin Ha, Andrew Roth, Daniel Lai, Ali Bashashati, Jiarui Ding, Rodrigo Goya, Ryan Giuliany, Jamie Rosner, Arusha Oloumi, Karey Shumansky, Suet-Feung Chin, Gulisa Turashvili, Martin Hirst, Carlos Caldas, Marco A Marra, Samuel Aparicio, and Sohrab P Shah. Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer. Genome Research, (advanced online publication), May 2012.

S P Shah, A Roth, R Goya, A Oloumi, G Ha, Y Zhao, G Turashvili, J Ding, K Tse, G Hafari, A Bashashati, L M Prentice, J Khattra, A Burleigh, D Yap, V Bernard, A McPherson, K Shuman- sky, A Crisan, R Giuliany, A Heravi-Moussavi, J Rosner, D Lai, I Birol, R Varhol, A Tam, N Dhalla, T Zeng, K Ma, S K Chan, M Griffth, A Moradian, S W Cheng, G B Morin, P Watson, K Gelmon, S Chia, S F Chin, C Curtis, O M Rueda, P D Pharoah, S Damaraju, J Mackey, K Hoon, T Harkins, V Tadigotla, M Sigaroudinia, P Gascard, T Tlsty, J F Costello, I M Meyer, C J Eaves, W W Wasserman, S Jones, D Huntsman, M Hirst, C Caldas, M A Marra, and S Aparicio. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature, 486(7403):395-399, Jun 2012.