Esempio n. 1
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    def pv_adj_and_ind(self, nperm, pv_adj, nullfit, lrt, lrtperm,
                       alteqnull, alteqnullperm, qmax, nullfitfile, nlocalperm):        
        if nlocalperm>0: #don't do the fitting
            ind = pv_adj.argsort()
            return pv_adj, ind

        from fastlmm.association.tests import Cv                
        return Cv.pv_adj_and_ind(nperm, pv_adj, nullfit, lrt, lrtperm,
                                 alteqnull, alteqnullperm, qmax, nullfitfile, nlocalperm) # call the shared version of this method
Esempio n. 2
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    def pv_adj_and_ind(self, nperm, pv_adj, nullfit, lrt, lrtperm,
                       alteqnull, alteqnullperm, qmax, nullfitfile, nlocalperm):        
        if nlocalperm>0: #don't do the fitting
            ind = pv_adj.argsort()
            return pv_adj, ind

        from fastlmm.association.tests import Cv                
        return Cv.pv_adj_and_ind(nperm, pv_adj, nullfit, lrt, lrtperm,
                                 alteqnull, alteqnullperm, qmax, nullfitfile, nlocalperm) # call the shared version of this method
Esempio n. 3
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def recalibrate(dirin,filepattern='*.txt', lrtpermfile=None, pnames=["P-value(50/50)"], rownames=rownames(), nullfit="qq",qmax=0.1, postfix="RECALIBRATED"):
    '''
    Read in each results file, use the null stats in lrtpermfile to re-calibrate the null distribution, 
    and then add a column to each file
    '''
    assert lrtpermfile is not None, "must provide lrtpermfile (output by FastLmmSet.py with lrt)"

    myfiles = getfiles(dirin, filepattern)
        
    ii=0
    for f in myfiles:       
        ii=ii+1
        print str(ii) + ") " + f
        pv,rowids,llnull,llalt = extractpvals(f,pnames,rownames)
        lrt = -2*(llnull-llalt)  
        alteqnull = (lrt==0)
        pv_adj = Cv.pv_adj_and_ind(nperm=0, pv_adj=None, nullfit=nullfit, lrt=lrt, lrtperm=None,
                                 alteqnull=alteqnull, alteqnullperm=None, qmax=qmax, 
                                 nullfitfile=lrtpermfile, nlocalperm=0, sort=False)[0]
        outfile = ut.appendtofilename(f,postfix)        
        np.savetxt(outfile, pv_adj)