README file for LSKM.R

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# License
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LSKM.R is a free software package; you can redistribute it and/or
modify it under the terms of the GNU General Public License version 2.
This software package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
Public License for more details.

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# Citing this work
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If you publish results using the methods implemented in LSKM.R, we
request that you reference the following paper in your manuscript:
Kwee et al. (2007) A Powerful and Flexible Multilocus Association Test
for Quantitative Traits. American Journal of Human Genetics 82:386-397

Multilocus Association Test for Quantiative Traits

LSKM.R is used for multilocus association testing of quantitative
traits. The method behind LSKM.R is based on least-squares kernel
machines and is described in Kwee et al., AJHG 82:386-397, 2008. 


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# Input files (examples provided in download):
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Important: All input files must be ASCII space-delimited.
The filenames given here are the defaults expected by the program;
they may be changed in the first few lines of the LSKM.R code. 

A) trait.dat:

    * One row for each individual plus a header row with trait label

    * One column containing quantitative trait values


B) genotype.dat:

    * One row for each individual plus a header row with genotype labels

    * One column for each SNP genotype listed in header row

    * Each genotype coded as number of copies of reference allele at SNP (0,1,2)

    * No missing values allowed
  

C) covariate.dat (not necessary if no environmental covariates exist):  

   * One row for each individual plus a header row with covariate labels

   * One column for each covariate listed in header row

     * Covariates can be categorical or continuous

     * No missing values allowed


IMPORTANT: The row ordering of subjects must be consistent among
trait.txt, genotype.txt, and covariate.txt. In other words, if the
trait outcome for subject i is in row k of trait.txt, then the
genotype data for subject i must be found in row k of genotype.txt. 


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# Output file:
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LSKM.out