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For the sparse matrix implementation, please install the R package as follows:
For the dense matrix implementation, please install the R package as follows:
summaryZ, The Z statistics of p SNPs from q GWA studies. A matrix with dimension p x q for p SNPs and q traits. The first column corresponds to the primary trait and the rest columns correspond to the secondary traits.
Nvec, A vector of length q for the sample sizes of q GWA studies.
plinkLD, LD matrix information.
NumIter, The number of maximum iterations for the estimation procedure.
funcIndex, Inputs for the functional annotations of SNPs. A p x k matrix with (0,1) entry; p is the number of SNPs and k is the number of functional annotations. For the element at i-th row, j-th column, the entry 0 means SNP i without j-th functional annotation; entry 1 means otherwise.
numfunc, The number of functional annotations.
dfMax The upper bound of the number of non-zero estimates of coefficients for the primary trait.
The current version only work on Unix, Linux and Mac System, R(>=3.4.3), R packages “gtools” and “permutations” and GCC(>=4.4.7) are required.
Modify the parameters in the gsfPEN.R, and execute it.
Please find it in the R package.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.