Format
This dataset contain three files: - CGHset
- a CGHcall object containing 8 cervical pre-curses cancer lesions.
These samples were taken from Bierkens et al. 2013 and available under GEO accession number GSE34575.
- CNVset
- a bed file with CNV locations as provided by http://dgv.tcag.ca/.
- calls_focals
- Complete results file after running focalCall on the example data
from Bierkens et al. 2013.
CGHset: A CGHcall object containing the following 8 samples:
- hgCIN.2.10_16
- high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.10_16.
- hgCIN.2.13_16
- high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.13_16.
- hgCIN.2.8_31
- high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.8_31.
- hgCIN.2.16_31
- high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.16_31.
- CIN3.1.2_16
- Cervical Intra-epithelial Neoplasia sample: CIN3.1.2_16.
- hgCIN.2.4_16
- high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.4_16.
- CIN3.1.8_16
- Cervical Intra-epithelial Neoplasia sample: CIN3.1.8_16.
- hgCIN.2.19_58
- high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.19_58.
CNVset: A bed file containing the following columns:
- CNV ID
- Identification ID for copy number variation (CNV)
- start
- Basepair position that indicates start of CNV
- end
- Basepair position that indicates end of CNV
calls_focals: results file after running focalCall on the samples described above:
- calls_focals
- results file of class
cghCall
Source
Bierkens, M., Krijgsman, O., Wilting, S.M., Bosch, L., Jaspers, A., Meijer, G.A., Meijer, C.J., Snijders, P.J., Ylstra, B., Steenbergen, R.D. (2013). Focal aberrations indicate EYA2 and hsa-miR-375 as oncogene and tumor suppressor in cervical carcinogenesis. Genes Chromosomes Cancer 52,56-68.