Simulated data was generated using the mvrnorm function in R and genotype matrix X. The two traits have correlation 0.4 and each has two causal variants, of which one, rs61839660 is shared between traits; trait 1 has second causal variant rs62626317 and trait 2 has second causal variant rs11594656. The traits are from a sample of 2000, with no missing measurements.
An object of class
list of length 7.
JAMmain.input was generated using the following command, where all called objects exist in the flashfm package, fstub and fstubJ are paths with file prefixes for output data, and path2plink is the path to the software plink JAMexpanded.multi(beta,X,snpinfo,ybar,diag(covY),N,chr=10,fstub=fstub,mafthr=0.005,path2plink="/software/plink",r2=0.99,save.path=fstubJ,related=FALSE,y=NULL)
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