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
data(tumour)
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.