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GreenwoodLab / RVPedigree

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RVPedigree() outputs the same p-value for each region #4

Open lckarssen opened 8 years ago

lckarssen commented 8 years ago

When running the RVPedigree() function on several regions, the output () for each region is the same. See for example section 4 (page 12) in the vignette:

gwresults <- RVPedigree(method="VCC1",
                        y=pheno,
                        X=covar,
                        Phi=rel.mat,
                        regions=genes,
                        filename=geno.file,
                        type='ped',
                        pvalThreshold=1
                        )
## Estimating null model...
## Null model estimated.
## Starting association analysis of the 3 regions...
## Warning in snpStats::read.pedfile(file = filename, snps = snps2out): 2 loci were monomorphic
## Warning in VCC1.region(y = y, X = X, Phi = Phi, type = type, filename = filename, : No genotypes available in the region from 9050050 to 9075000 on chromosome 20

gwresults
##         Score.Test  P.value    N.Markers
## Gene_1  1768.63     0.3195559  4
## Gene_2  1768.63     0.3195559  6

At first glance this seems to happen regardless of the method (ASKAT, VCC1, ...) used.