RBPMotif-class {transite} | R Documentation

## An S4 class to represent a RBPMotif

### Description

An S4 class to represent a RBPMotif

Getter Method motifId

Getter Method motifRbps

Getter Method motifMatrix

Getter Method motifHexamers

Getter Method motifHeptamers

Getter Method motifLength

Getter Method motifIUPAC

Getter Method motifType

Getter Method motifSpecies

Getter Method motifSource

### Usage

    motifId(object)

    ## S4 method for signature 'RBPMotif'
    motifId(object)

    motifRbps(object)

    ## S4 method for signature 'RBPMotif'
    motifRbps(object)

    motifMatrix(object)

    ## S4 method for signature 'RBPMotif'
    motifMatrix(object)

    motifHexamers(object)

    ## S4 method for signature 'RBPMotif'
    motifHexamers(object)

    motifHeptamers(object)

    ## S4 method for signature 'RBPMotif'
    motifHeptamers(object)

    motifLength(object)

    ## S4 method for signature 'RBPMotif'
    motifLength(object)

    motifIUPAC(object)

    ## S4 method for signature 'RBPMotif'
    motifIUPAC(object)

    motifType(object)

    ## S4 method for signature 'RBPMotif'
    motifType(object)

    motifSpecies(object)

    ## S4 method for signature 'RBPMotif'
    motifSpecies(object)

    motifSource(object)

    ## S4 method for signature 'RBPMotif'
    motifSource(object)

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

    ## S4 method for signature 'RBPMotif,ANY'
    plot(x)

### Arguments

`object` | RBPMotif object
`x` | RBPMotif object

### Value

Object of type RBPMotif

### Slots

`id`

  motif id (character vector of length 1)

`rbps`

  character vector of names of RNA-binding proteins associated with this motif

`matrix`

  data frame with four columns (A, C, G, U) and 6 - 15 rows (positions), where cell (i, j) contains weight of nucleotide j on position i

`hexamers`

  character vector of hexamers associated with this motif

`heptamers`

  character vector of heptamers associated with this motif

`length`

  length of the motif (i.e., `nrow(matrix)`)

`iupac`

  IUPAC code for motif matrix (see `generateIUPACByMatrix`)

`type`

  type of motif (e.g., `'HITS-CLIP'`, `'EMSA'`, `'SELEX'`, etc.)

`species`

  species where motif was discovered (e.g., `'Homo sapiens'`)

`src`

  source of motif (e.g., `'RBPDB v1.3.1'`)

### Examples

    kmers <- c("AAAAAAA", "CAAAAAA")
    iupac <- generateIUPACByKmers(kmers,
      code = initIUPAClookupTable())
    hexamers <- generateKmersFromIUPAC(iupac, 6)
    heptamers <- generateKmersFromIUPAC(iupac, 7)
    new("RBPMotif", id = "custom.motif", rbps = "RBP1",
      matrix = NULL, hexamers = hexamers, heptamers = heptamers, length = 7L,
      iupac = iupac, type = "HITS-CLIP", species = "Homo sapiens", src = "user"
    )

[Package transite version 1.0.2 Index]