Package 'neuroblastoma'

Title: Neuroblastoma Copy Number Profiles
Description: Annotated neuroblastoma copy number profiles, a benchmark data set for change-point detection algorithms, as described by Hocking et al. <doi:10.1186/1471-2105-14-164>.
Authors: Toby Dylan Hocking [aut, cre]
Maintainer: Toby Dylan Hocking <[email protected]>
License: GPL-3
Version: 2023.9.3
Built: 2024-11-05 05:27:29 UTC
Source: https://github.com/tdhock/neuroblastoma

Help Index

Neuroblastoma copy number profiles and breakpoint annotations

Description

Tumors from patients at the Institut Curie were assayed using array comparative genomic hybridization. Their normalized copy number profiles are available as neuroblastoma$profiles and the breakpoint annotations are available as neuroblastoma$annotations.

Usage

data(neuroblastoma)

Format

A named list of 2 data frames:

profiles

A data.frame with one row for each probe, and these variables:

profile.id

factor: id of copy number profile.

chromosome

factor: chromosome on which the probe was mapped.

position

integer: probe was mapped to this position in base pairs.

logratio

numeric: normalized logratio of the probe, which should be proportional to copy number.

annotations

a data.frame with one row for each annotated region, and these variables:

profile.id

factor: id of copy number profile.

chromosome

factor: chromosome of this annotation.

min

integer: lower limit of this region in base pairs.

max

integer: upper limit of this region in base pairs.

annotation

factor: annotation of this region, either "normal" for no breakpoints or "breakpoint" for at least one breakpoint.

Source

Gudrun Schleiermacher and Isabelle Janoueix-Lerosey, Institut Curie.