BierkensCNA: Cervical cancer arrayCGH data

In focalCall: Detection of focal aberrations in DNA copy number data

Description

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).

Usage

BierkensCNA

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

Value

Three datasets are returned as described in the section above.

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.

Examples

# Load the data file
data(BierkensCNA)

Example output

Loading required package: CGHcall
Loading required package: impute
Loading required package: DNAcopy
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: CGHbase
Loading required package: marray
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: snowfall
Loading required package: snow

Attaching package: 'snow'

The following objects are masked from 'package:BiocGenerics':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster


Attaching package: 'CGHcall'

The following object is masked from 'package:BiocGenerics':

    normalize

focalCall documentation built on April 28, 2020, 9:09 p.m.