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.
fm2
An object of class list of length 2.
fm2 was generated using the following command, where all called objects exist in the flashfm package, fstub is a file prefix for FINEMAP input/output files, and FMpath is the path to the software FINEMAP fm2 <- FLASHFMwithFINEMAP(gwas.list,corX,raf,ybar,N,fstub="DIRresults/eg",TOdds=1,covY,cpp=.99,NCORES=2,FMpath="/software/finemap_v1.4_x86_64/finemap_v1.4_x86_64") 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)