RBPMotif-class {transite} | R Documentation |
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
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)
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 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'
)
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" )