HMMcopy example dataset


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 where reads mapped to multiple sites were ignored.


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


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


Normal copy number profile generated via correctReadcount


Parameters for segmenting ‘tumour_copy’ in HMMsegment


Segmented output of ‘tumour_copy’ HMMsegment

using ‘tumour_param’




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

‘tumour_param’ is a numeric matrix.

‘tumour_segments’ is a list.


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.

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