BierkensCNA {focalCall} | R Documentation |
Example dataset with arrayCGH data of cervical pre-cancer lesions. OF NOTE: this set contains only 8 samples from the data and only the complete probeset for chromosome 2. Complete dataset is available from GEO (GSE34575).
BierkensCNA
This dataset contain three files:
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.
a bed file with CNV locations as provided by http://dgv.tcag.ca/.
Complete results file after running focalCall on the example data from Bierkens et al. 2013.
CGHset: A CGHcall object containing the following 8 samples:
high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.10_16.
high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.13_16.
high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.8_31.
high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.16_31.
Cervical Intra-epithelial Neoplasia sample: CIN3.1.2_16.
high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.4_16.
Cervical Intra-epithelial Neoplasia sample: CIN3.1.8_16.
high-grade Cervical Intra-epithelial Neoplasia sample: hgCIN.2.19_58.
CNVset: A bed file containing the following columns:
Identification ID for copy number variation (CNV)
Basepair position that indicates start of CNV
Basepair position that indicates end of CNV
calls_focals: results file after running focalCall on the samples described above:
results file of class cghCall
Three datasets are returned as described in the section above.
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.
# Load the data file data(BierkensCNA)