Colocalisation testing supplying only regression coefficients and their variancecovariants matrices
1 2 3 4 
b1 
regression coefficients for trait 1 
b2 
regression coefficients for trait 2 
V1 
variancecovariance matrix for trait 1 
V2 
variancecovariance matrix for trait 2 
k 
Theta has a Cauchy(0,k) prior. The default, k=1, is equivalent to a uniform (uninformative) prior. We have found varying k to have little effect on the results. 
plot.coeff 

bma 
parameter set to 
plots.extra 
list with 2 named elements, x and y, equal length character vectors containing the names of the quantities to be plotted on the x and y axes.

bayes 
Logical, indicating whether to perform
Bayesian inference for the coefficient of
proportionality, eta. If 
bayes.factor 
Calculate Bayes Factors to compare
specific values of eta. 
level.ci,n.approx 

Typically this should be called from
coloc.test()
or coloc.bma()
,
but is left as a public function, to use at your own
risk, if you have some other way to define the SNPs under
test.
an object of class coloc, colocBayes or colocBMA
Chris Wallace
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