test.data: Test data - copy number profiles

In arnevpladsen/CARMA: Calculate CARMA scores

Description

A test data file containing segmented copy number profiles from 100 breast cancer samples, for test running the CARMA algorithm. The test data are assembled from real tumor profiles, by randomly combining chromosome-specific copy number profiles from multiple samples to construct new whole genome copy number profiles.

Usage

test.data

Format

List of 100 data frames, each containing the following 5 columns:

chr

a charachter giving the chromosome

startpos

a numeric vector giving the hg19 start position of the segment

endpos

a numeric vector giving the hg19 end position of the segment

nMajor

a numeric vector giving the major allele integer copy number state for the segment

nMinor

a numeric vector giving the minor allele integer copy number state for the segment

Examples

test.results = CARMA(test.data, region.type="arm", hg.version="hg19")
carma.summary = summaryCARMA(test.results)

arnevpladsen/CARMA documentation built on Dec. 19, 2021, 4:39 a.m.