getGenomeAndMask {regioneR} | R Documentation

## getGenomeAndMask

### Description

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.

### Note

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

### See Also

`getMask`, `getGenome`, `characterToBSGenome`, `maskFromBSGenome`, `emptyCacheRegioneR`

### Examples

    getGenomeAndMask("hg19", mask=NA)

    getGenomeAndMask(genome=data.frame(c("chrA", "chrB"), c(15000000, 10000000)), mask=NA)

[Package regioneR version 1.16.5 Index]