Example of copy number log ratio dataset

Source: R/CNprep.R

Log ratio data for 5 breast cancer genomes, derived using Representational Oligonucleotide Microarray Analysis (ROMA), an array-based hybridization method that uses genomic complexity reduction based on representations.

data(ratexample)

Format

a log ratio matrix with 83055 rows, one per oligonucleotide probe, and 5 columns, one for each breast tumor sample.

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

Value

a log ratio matrix with 83055 rows, one per oligonucleotide probe, and 5 columns, one for each breast tumor sample.

Details

The values are natural log copy number ratios, consistent with data in segexample (segmented data for these tumors) and normsegs. These copy number ratios are normalized using an intensity-based lowess curve fitting algorithm.

See also

  • CNpreprocessing for pre-process DNA copy number (CN) data for detection of CN events.

  • makeCNPmask for creating a mask given a set of copy number events.

  • applyCNPmask for applying a mask to a set of copy number events.

Examples


## Loading log ratio dataset
data(ratexample)

## Plot the whole genome log ratio data for the first profile "WZ1"
## Note X and Y chromosomes at the far right of the plot
plot(ratexample[,"WZ1"], ylab="log ratio", xlab="position")