Enhancers-class {enhancerHomologSearch} | R Documentation

## Class `"Enhancers"`

### Description

An object of class "Enhancers" represents the output of function getENCODEdata, which includes the sequences of enhancers and their genomic coordinates.

### Usage

    Enhancers(genome, peaks, TFBP, TFBP0)

    ## S4 method for signature 'Enhancers'
    x$name

    ## S4 replacement method for signature 'Enhancers'
    x$name <- value

    ## S4 method for signature 'Enhancers,ANY'
    distance(x)

    ## S4 replacement method for signature 'Enhancers'
    distance(x) <- value

    ## S4 method for signature 'Enhancers'
    tfbp(x)

    ## S4 method for signature 'Enhancers'
    query_tfbp(x)

    ## S4 method for signature 'Enhancers'
    getSeq(x, ...)

    ## S4 method for signature 'Enhancers,ANY'
    subsetByOverlaps(
      x,
      ranges,
      maxgap = -1L,
      minoverlap = 0L,
      type = c("any", "start", "end", "within", "equal"),
      invert = FALSE,
      ...
    )

    ## S4 method for signature 'Enhancers'
    subset(x, ...)

    ## S4 method for signature 'Enhancers'
    seqinfo(x)

    ## S4 method for signature 'Enhancers'
    genome(x)

    ## S4 replacement method for signature 'Enhancers'
    genome(x) <- value

    ## S4 method for signature 'Enhancers'
    peaks(x)

    ## S4 replacement method for signature 'Enhancers'
    peaks(x) <- value

    ## S4 method for signature 'Enhancers'
    show(object)

### Arguments

`genome` | An object of BSgenome.
`peaks` | An object of GRanges.
`TFBP` | An object of lgCMatrix.
`TFBP0` | An vector of logical. `"Enhancers"`
`x` | An object of `"Enhancers"`
`name` | Slot name.
`value` | The values.
`...` | parameters can be passed to upstream functions.
`ranges, maxgap, minoverlap, type, invert` | parameters used by subsetByOverlaps
`object` | An object of `"Enhancers"`

### Value

An object of Enhancers.

### Slots

`genome`

  An object of BSgenome.

`peaks`

  An object of GRanges.

`TFBP`

  An object of lgCMatrix.

`TFBP0`

  An vector of logical.

### Examples

    Enhancers()

[Package enhancerHomologSearch version 1.0.1 Index]