Description Usage Arguments Value Note See Also Examples
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.
1 | getGenomeAndMask(genome, mask=NULL)
|
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 |
A list with two elements: genome and mask. Genome and mask are GRanges objects.
This function is memoised (cached) using the memoise
package. To empty the cache, use forget(getGenomeAndMask)
getMask
, getGenome
, characterToBSGenome
, maskFromBSGenome
, emptyCacheRegioneR
1 2 3 | getGenomeAndMask("hg19", mask=NA)
getGenomeAndMask(genome=data.frame(c("chrA", "chrB"), c(15000000, 10000000)), mask=NA)
|
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