RBPMotif-class {transite} | R Documentation

## An S4 class to represent a RBPMotif

### Description

An S4 class to represent a RBPMotif

Getter Method get_id

Getter Method get_rbps

Getter Method get_motif_matrix

Getter Method get_hexamers

Getter Method get_heptamers

Getter Method get_width

Getter Method get_iupac

Getter Method get_type

Getter Method get_species

Getter Method get_source

### Usage

    get_id(object)

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

    get_rbps(object)

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

    get_motif_matrix(object)

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

    get_hexamers(object)

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

    get_heptamers(object)

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

    get_width(object)

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

    get_iupac(object)

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

    get_type(object)

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

    get_species(object)

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

    get_source(object)

    ## S4 method for signature 'RBPMotif'
    get_source(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 `generate_iupac_by_matrix`)

`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 <- generate_iupac_by_kmers(kmers,
      code = init_iupac_lookup_table())
    hexamers <- generate_kmers_from_iupac(iupac, 6)
    heptamers <- generate_kmers_from_iupac(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 1.10.0 Index]