getMask

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Description

Function to obtain a mask given a genome available as a BSgenome. The mask returned is the merge of all the active masks in the BSgenome.

Since it uses characterToBSGenome, the genome can be either a BSgenome object or a character string uniquely identifying the a BSgenome object installed.

Usage

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getMask(genome)

Arguments

genome

the genome from where the mask will be extracted. It can be either a BSgenome object or a character string uniquely identifying a BSgenome object installed (e.g. "hg19", "mm10", ...)

Value

A GRanges object with the genomic regions to be masked out

Note

This function is memoised (cached) using the memoise package. To empty the cache, use forget(getMask)

See Also

getGenome, getGenomeAndMask, characterToBSGenome, maskFromBSGenome, emptyCacheRegioneR

Examples

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hg19.mask <- getMask("hg19")

hg19.mask

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