Description Usage Arguments Details Value See Also
Perform an informed GenomeWide Association Study (iGWAS). This is based on a current study and a prior study. The goal is to discover significant SNPs in the current study using hypothesis testing. The prior study is used to improve power. Pvalues and sample sizes are used for both the current and the prior studies.
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P_current 
Pvalues in the current study, a numeric vector of length J, with entries between 0 and 1 
N_current 
sample size in the current study, a positive integer (or vector of length J) 
P_prior 
Pvalues in the prior study, a numeric vector of length J, with entries between 0 and 1 
N_prior 
sample size in the current study, a positive integer (or vector of length J) 
q 
(optional) uncorrected level at which tests should be performed. Default 
weighting_method 
(optional) weighting method used. Available methods: 
p_adjust_method 
(optional) adjustment method for multiple testing used. The available methods are

sides 
(optional) The prior pvalues must be one or twosided: sides = 1 or 2. Default 
phi 
(optional) dispersion factor used to multiply all standard errors. Default 
beta 
(optional) weights are proportional to 
UB_exp 
(optional) upper bound on the weights (default 
figure 
(optional) 
GWAS_data_frame 
(optional) when 
This method computes the pvalue weights based on the prior pvalues, and uses them in multiple testing (pvalue weighting) for the current pvalues. The pvalue weighting method (e.g. Unweighted, Bayes) and the multiple testing adjustment (e.g. Bonferroni, BenjaminiHochberg) can be specified independently.
For more details, see the paper "Optimal Multiple Testing Under a Gaussian Prior on the Effect Sizes", by Dobriban, Fortney, Kim and Owen, http://arxiv.org/abs/1504.02935
A list containing:
sig_ind
: A vector of 01s indicating the significant tests (1s)
num_sig
: The number of significant tests. Equals sum(sig_ind)
w
: The computed pvalue weights
P_w
: The weighted pvalues. These equal P_current/w
Other p.value.weighting: bayes_weights
;
exp_weights
;
spjotvoll_weights
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