RBPMotif-class {transite} | R Documentation |
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
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)
object |
RBPMotif object |
x |
RBPMotif object |
Object of type RBPMotif
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'
)
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" )