In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. A user-friendly interface (SNPSpD) for performing this correction is available online (http://genepi.qimr.edu.au/general/daleN/SNPSpD/). Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.
%0 Generic
%1 nyholt2004simple
%A Nyholt, Dale R.
%D 2004
%I University of Chicago Press
%J American journal of human genetics
%K SNP linkage population_genomics statistics
%N 4
%P 765--769
%T A Simple Correction for Multiple Testing for Single-Nucleotide Polymorphisms in Linkage Disequilibrium with Each Other
%U http://linkinghub.elsevier.com/retrieve/pii/S000292970761903X
%V 74
%X In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. A user-friendly interface (SNPSpD) for performing this correction is available online (http://genepi.qimr.edu.au/general/daleN/SNPSpD/). Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.
@misc{nyholt2004simple,
abstract = {In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. A user-friendly interface (SNPSpD) for performing this correction is available online (http://genepi.qimr.edu.au/general/daleN/SNPSpD/). Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.},
added-at = {2012-09-08T22:24:55.000+0200},
author = {Nyholt, Dale R.},
biburl = {https://www.bibsonomy.org/bibtex/27548f945ad484a879e2d1b6dbedd3f4e/peter.ralph},
interhash = {76fe6441365e1c48d71b6786aeb2b0bc},
intrahash = {7548f945ad484a879e2d1b6dbedd3f4e},
issn = {00029297},
journal = {American journal of human genetics},
keywords = {SNP linkage population_genomics statistics},
month = apr,
number = 4,
pages = {765--769},
publisher = {University of Chicago Press},
refid = {S0002-9297(07)61903-X
DOI - 10.1086/383251},
timestamp = {2012-09-08T22:24:56.000+0200},
title = {A Simple Correction for Multiple Testing for Single-Nucleotide Polymorphisms in Linkage Disequilibrium with Each Other},
url = {http://linkinghub.elsevier.com/retrieve/pii/S000292970761903X},
volume = 74,
year = 2004
}