hapmapSegments | R Documentation |
Data from 225 HapMap control samples that has been analyzed with DNAcopy to identify segments and record information about copy number variaiton.
data(hapmapSegments)
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.
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]
[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.
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