neuroblastomaDetailed: Detailed annotations of the neuroblastoma data
In tdhock/bams: Breakpoint annotation model smoothing

Description Usage Format Details Source

An annotation is the number of breakpoints that an expert expects of a segmentation model in a certain region, after visual inspection of the scatterplot of data.

1	data(neuroblastomaDetailed)

A data frame with 4359 observations on the following 5 variables.

profile.id: a factor with levels corresponding to the profile.id column of neuroblastoma$profiles.
chromosome: idem for neuroblastoma$chromosome.
min: first position of the annotated region in base pairs.
max: idem for the last position.
annotation: factor indicating the number of breakpoints in this region: >0breakpoints means at least one breakpoint, 1breakpoint means exactly 1 breakpoint, normal means exactly 0 breakpoints.

The neuroblastoma data are a set of 575 DNA copy number profiles of neuroblastoma tumors, available as data(neuroblastoma,package="neuroblastoma"). That package provides the "original" set of up to 6 annotated regions per profile as neuroblastoma$annotations. There is at most 1 annotation per chromosome, and 2 types of annotations: breakpoint means 1 or more breakpoints and normal means exactly 0 breakpoints. These data were made by Gudrun Schleiermacher and Isabelle Janoueix-Lerosey, by typing 0 or 1 in a spreadsheet after visual inspection of the profiles.

This package provides a different set of annotations of the same data. We say they are detailed since there is often more than 1 annotation per chromosome, and there is another type of annotation: 1breakpoint means there is exactly 1 breakpoint in that region. These annotations were created by Toby Dylan Hocking and Valentina Boeva using GUIs which allow drawing regions on the plotted data.

http://cbio.ensmp.fr/~thocking/neuroblastoma/annotations.csv

tdhock/bams documentation built on May 31, 2019, 7:34 a.m.