Function to obtain a valid genome and mask pair given a valid genome identifier and optionally a mask.
If the genome is not a BSgenome object or a character string uniquely identifying a BSgenome package installed, it will return the genome "as is". If a mask is provided, it will simply return it. Otherwise it will return the mask returned by getMask(genome) or an empty mask if genome is not a valid BSgenome or BSgenome identifier.
Usage
getGenomeAndMask(genome, mask=NULL)
Arguments
genome
the genome object or genome identifier.
mask
the mask of the genome in a valid RS format (data.frame, GRanges, BED-like file...). If mask is NULL, it will try to get a mask from the genome. If mask is NA it will return an empty mask. (Default=NULL)
Value
A list with two elements: genome and mask. Genome and mask are GRanges objects.