QIMR Genetic Epidemiology Laboratory Home > Dale's Homepage > SNPSpDlite

Single Nucleotide Polymorphism Spectral Decomposition Lite (SNPSpDlite)

SNPSpDlite takes the same input at SNPSpD, but ONLY outputs the LD correlation matrix, Meff and MeffLi estimates and GOLD input (i.e., does not perform time-consuming varimax/promax rotations) thus allowing users to obtain Meff/MeffLi values for large numbers (1000s) of SNPs.

Users may also be interested in the related site (SNPSpDsuperlite) which is an even leaner version of SNPSpD.

Users may also be interested in the related site (matSpD) which only requires users to upload a correlation matrix.

Please use the following reference when reporting results based on SNPSpD:
Nyholt DR (2004) A simple correction for multiple testing for SNPs in linkage disequilibrium with each other. Am J Hum Genet 74(4):765-769.
 

To run SNPSpD using all fully genotyped family members:

Please specify where your "merlin.pre" file is located:

Please specify where your "merlin.map" file is located:

Please be patient, the spectral decomposition will take a few moments.

 
To run SNPSpD using fully genotyped founders only:

Please specify where your "merlin.pre" file is located:

Please specify where your "merlin.map" file is located:

Please be patient, the spectral decomposition will take a few moments.


 

To run SNPSpD using all family members:

Please specify where your "merlin.pre" file is located:

Please specify where your "merlin.map" file is located:

Please be patient, the spectral decomposition will take a few moments.

 
To run SNPSpD using founders only:

Please specify where your "merlin.pre" file is located:

Please specify where your "merlin.map" file is located:

Please be patient, the spectral decomposition will take a few moments.


 
 
Page last updated March 14, 2007.
 
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