copyNumbersSegmented: Segmented data of two tumor samples

In tgac-vumc/ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Segmented data of two tumor samples

Description

A QDNAseq-object with segmented copy number data of two tumor samples: 'sample1' and 'sample2'

Usage

data("copyNumbersSegmented")

Format

A QDNAseqCopyNumbers S4 object with 3113 features (bins), each represented by copy number values and segment values of two samples

copyNumbersSegmented@assayData$copynumber

copy number data saved in a matrix, rownames are bins (chr:start-end), colnames are sampleNames

copyNumbersSegmented@assayData$segmented

segment values saved in a matrix, the rownames are bins (chr:start-end), colnames are sampleNames

Value

A QDNAseqCopyNumbers S4 object

Examples

data("copyNumbersSegmented")
## ploidyplotloop(copyNumbersSegmented, currentdir = ".")
singlemodel(copyNumbersSegmented, QDNAseqobjectsample = 1)
singleplot(copyNumbersSegmented, 1, cellularity = 0.79)
model2 <- singlemodel(copyNumbersSegmented, QDNAseqobjectsample = 2)
singleplot(copyNumbersSegmented, 2, cellularity = with(model2, 
  minima[which(rerror==min(rerror))]))

tgac-vumc/ACE documentation built on Nov. 29, 2022, 12:15 a.m.