CNprep (version 2.2)

segexample: Example of a segmented copy number table.

Description

Segmented log ratio data for 5 breast cancer genomes, derived using Representational Oligonucleotide Microarray Analysis (ROMA) platform. ROMA detects genomic amplifications and deletions with boundaries defined at a resolution of 50 kb. In this segmented table, each row represnts a segment.

Usage

data(segexample)

Format

A data frame with 479 rows/segments and 12 columns/variables.

ID

a character vector of profile IDs

start

a numeric vector (segment start probe number)

end

a numeric vector (segment end probe number)

num.probes

a numeric vector (number of probes in the segment)

seg.median

a numeric vector (median log ratio)

chrom

a numeric vector (chromosome number)

chrom.pos.start

a numeric vector (genomic start)

chrom.pos.end

a numeric vector (genomic end)

cytoband.start

a character vector (cytogenetic band start)

cytoband.end

a character vector (cytogenetic band end)

abs.pos.start

a numeric vector (genomic start, absolute)

abs.pos.end

a numeric vector (genomic end, absolute)

Details

Segment medians are computed from log copy number ratio. The corresponding raw data table is ratexample in this package.

Examples

# NOT RUN {
data(segexample)
# }