BSParams-class {BSgenome} | R Documentation

## Class "BSParams"

### Description

A parameter class for representing all parameters needed for running the `bsapply` method.

### Objects from the Class

Objects can be created by calls of the form `new("BSParams", ...)`.

### Slots

`X`:

  a BSgenome object that contains chromosomes that you wish to apply FUN on

`FUN`:

  the function to apply to each chromosome in the BSgenome object 'X'

`exclude`:

  this is a character vector with strings that will be treated as regular expressions to filter out chromosomes whose names match these strings.

`simplify`:

  TRUE/FALSE value to indicate whether or not the function should try to simplify the output for you.

`maskList`:

  A named logical vector of maskStates preferred when used with a BSGenome object. When using the bsapply function, the masks will be set to the states in this vector.

`motifList`:

  A character vector which should contain motifs that the user wishes to mask from the sequence.

`userMask`:

  A IntegerRangesList object, where each element masks the corresponding chromosome in `X`. This allows the user to conveniently apply masks besides those included in `X`.

`invertUserMask`:

  A `logical` indicating whether to invert each mask in `userMask`.

### Methods

`bsapply(p)`

  Performs the function FUN using the parameters contained within `BSParams`.

### Author(s)

Marc Carlson

### See Also

`bsapply`

[Package BSgenome version 1.58.0 Index]