Enhancers-class: Class '"Enhancers"'

In jianhong/enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer

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()

jianhong/enhancerHomologSearch documentation built on Nov. 4, 2024, 8:29 p.m.