Check generic functions

[hofnerb]

Sometimes we have

setGeneric(function_name, function(object, ...)  standardGeneric('function_name'))

but then use e.g.

setMethod('function_name', definition = function(GWASdata, ...))

Shouldn't we use GWASdata (in this example) directly in the setGeneric to allow a proper dispatch? I fixed this for calc_kernel where the dispatch didn't work but it needs to be check for other functions as well (I think).

[jmanitz]

I think I cleaned the generics up. I had to change a lot and add a couple of generics. I hope the code still works. I couldnt test every function, in particular the ones playing around with gene annotation etc.

@sfriedrichs: Please check whether I used the correct signature. You can also use basic classes like numeric, character and matrix, or objects defined