hapmapSegments: Segmented HapMap Copy Number Data

hapmapSegmentsR Documentation

Segmented HapMap Copy Number Data

Description

Data from 225 HapMap control samples that has been analyzed with DNAcopy to identify segments and record information about copy number variaiton.

Usage

data(hapmapSegments)

Format

A data frame (hapmapSegments), with seven columns and 61,163 rows. This object contains the results of performing a segmentation copy number analysis (using DNAcopy). The seven columns are:

loc.start

The starting base position of the segment.

loc.end

The ending base postion of the segment.

seg.median

The median log R ratio across the segment.

SamID

The HapMap sample ID.

chrom

The chromosome on which the segment is located, stored as a single character in {1, 2, .., 22, X, Y}.

AvgBAF

The average B allele frequency across the segment.

num.mark

The number of markers (i.e., measured SNPs) located in the segment.

Source

BeadChip readings derived from 225 HapMap controls assessed on Human610-Quadv1 BeadChips were downloaded from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo; accession number GSE17205, 73 CEU samples; accession number GSE17206, 75 CH + JP; accession number GSE17207, 77 YRI). Raw BeadChip data from 168 patients with CLL and 225 HapMap controls were preprocessed to decode SNP/probe positions and generate genotype calls, log R ratio, and B-allele frequency (BAF) estimates using Illumina GenomeStudio, version 2010.2 (Illumina Inc.). Further processing to produce the segmentation results is described in the paper by Schweighofer et al. [1]

References

[1] Schweighofer CD, Coombes KR, Majewski T, Barron LL, Lerner S, Sargent RL, O'Brien S, Ferrajoli A, Wierda WG, Czerniak BA, Medeiros LJ, Keating MJ, Abruzzo LV. Genomic variation by whole-genome SNP mapping arrays predicts time-to-event outcome in patients with chronic lymphocytic leukemia: a comparison of CLL and HapMap genotypes. J Mol Diagn. 2013 Mar;15(2):196-209.

[2] International HapMap Consortium. The International HapMap Project. Nature. 2003 Dec 18;426(6968):789-96.


CloneData documentation built on July 1, 2022, 3 a.m.