RBPMotif-class: An S4 class to represent a RBPMotif

In transite: RNA-binding protein motif analysis

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"
)

transite documentation built on Nov. 8, 2020, 5:27 p.m.