Description Usage Arguments Value Examples
Fit the MAMBA model.
1 2 3 |
betajk |
Mxk matrix of effect size estimates, where row j corresponds to j-th SNP, and column k corresponds to k-th study . Missing values can be represented with NA. |
sjk2 |
Mxk matrix of effect size estimate variances, where row j corresponds to SNP j, and column k corresponds to study k. Missing values can be represented with NA. |
p |
initial value for EM algorithm, for the proportion of non-zero SNPs |
lambda |
initial value for EM algorithm, for the proportion of non-replicable SNPs which are well behaved, or non-outliers. |
tau2 |
initial value for EM algorithm, for the variance of replicable non-zero effect SNPs. |
alpha |
initial value for EM algorithm, for the variance inflation of outlier summary statistics at non-replicable SNPs. |
rel.eps |
threshold for when to end EM algorithm. rel.eps = (ll[i] - ll[i-1])/ll[i], where ll[i] is the log-likelihood at iteration i. |
snpids |
an optional vector of SNP id names. If not provided, the ID's will be 1:M, corresponding to the order of the matrix betajk. |
maxIter |
maximum # of EM iterations. |
A list containing
1 2 | d<-generate_data_mamba()
mod<-mamba(betajk=d$betajk, sjk2=d$sjk2)
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