segexample: Example of a segmented copy number table
In KrasnitzLab/CNprep: Pre-process DNA Copy Number (CN) Data for Detection of CN Events

segexample

R Documentation

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 represents 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.

Value

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)

Source

Hicks, J. et al. Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res. 2006. 16:1465–1479. doi: 10.1101/gr.5460106

Examples


## Loading log ratio dataset
data(segexample)

## Load datasets
data(segexample)
data(ratexample)
data(normsegs)

## Preprocess segments for WZ2 sample
segtable <- CNpreprocessing(segall=segexample[segexample[,"ID"] == "WZ2",],
                 ratall = ratexample, idCol = "ID", startCol = "start", 
                 endCol = "end", chromCol = "chrom", 
                 bpStartCol = "chrom.pos.start", 
                 bpEndCol = "chrom.pos.end", blsize = 50, 
                 minJoin = 0.25, cWeight = 0.4,
                 bsTimes = 30, chromRange = 1:22, nJobs = 1,
                 modelNames = "E", normalLength = normsegs[,1], 
                 normalMedian = normsegs[,2])

KrasnitzLab/CNprep documentation built on May 28, 2022, 8:32 p.m.