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

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"
)