Class "Enhancers"

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

Enhancers(genome, peaks, TFBP, TFBP0)

# S4 method for Enhancers
$(x, name)

# S4 method for Enhancers
$(x, name) <- value

# S4 method for Enhancers,ANY
distance(x)

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

# S4 method for Enhancers
tfbp(x)

# S4 method for Enhancers
query_tfbp(x)

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

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

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

# S4 method for Enhancers
seqinfo(x)

# S4 method for Enhancers
genome(x)

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

# S4 method for Enhancers
peaks(x)

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

# S4 method for 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()
#> This is an empty object of Enhancers.