universalmotif-class {universalmotif} | R Documentation |
Container for motif objects. See create_motif()
for creating
motifs as well as a more detailed description of the slots. For a
brief description of available methods, see examples
.
## S4 method for signature 'universalmotif,ANY,ANY,ANY' x[i] ## S4 replacement method for signature 'universalmotif,ANY,ANY,ANY' x[i] <- value ## S4 method for signature 'universalmotif' initialize(.Object, name, altname, family, organism, motif, alphabet = "DNA", type, icscore, nsites, pseudocount = 0.8, bkg, bkgsites, consensus, strand = "+-", pval, qval, eval, multifreq, extrainfo) ## S4 method for signature 'universalmotif' show(object) ## S4 method for signature 'universalmotif' as.data.frame(x) ## S4 method for signature 'universalmotif' subset(x, select) ## S4 method for signature 'universalmotif' normalize(object) ## S4 method for signature 'universalmotif' rowMeans(x) ## S4 method for signature 'universalmotif' colMeans(x) ## S4 method for signature 'universalmotif' colSums(x) ## S4 method for signature 'universalmotif' rowSums(x) ## S4 method for signature 'universalmotif' nrow(x) ## S4 method for signature 'universalmotif' ncol(x) ## S4 method for signature 'universalmotif' colnames(x) ## S4 method for signature 'universalmotif' rownames(x) ## S4 method for signature 'universalmotif' cbind(..., deparse.level = 0)
x |
universalmotif Motif. |
i |
|
value |
Object to replace slot with. |
.Object |
universalmotif Final motif. |
name |
|
altname |
|
family |
|
organism |
|
motif |
|
alphabet |
|
type |
|
icscore |
|
nsites |
|
pseudocount |
|
bkg |
|
bkgsites |
|
consensus |
|
strand |
|
pval |
|
qval |
|
eval |
|
multifreq |
|
extrainfo |
|
object |
universalmotif Motif. |
select |
|
... |
universalmotif Motifs. |
deparse.level |
Unused. |
A motif object of class universalmotif.
name
character(1)
altname
character(1)
family
character(1)
organism
character(1)
motif
matrix
alphabet
character(1)
type
character(1)
icscore
numeric(1)
Generated automatically.
nsites
numeric(1)
pseudocount
numeric(1)
bkg
numeric
Length equal to number of letters in alphabet.
bkgsites
numeric(1)
consensus
character
Generated automatically.
strand
character(1)
pval
numeric(1)
qval
numeric(1)
eval
numeric(1)
multifreq
list
extrainfo
character
Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca
## [ ## Access the slots. motif <- create_motif() motif["motif"] # you can also access multiple slots at once, released as a list motif[c("motif", "name")] ## [<- ## Replace the slots. motif["name"] <- "new name" # some slots are protected # motif["consensus"] <- "AAAA" # not allowed ## c ## Assemble a list of motifs. c(motif, motif) ## as.data.frame ## Represent a motif as a data.frame. The actual motif matrix is lost. ## Necessary for `summarise_motifs`. as.data.frame(motif) ## subset ## Subset a motif matrix by column. subset(motif, 3:7) # extract motif core ## normalize ## Apply the pseudocount slot (or `1`, if the slot is set to zero) to the ## motif matrix. motif2 <- create_motif("AAAAA", nsites = 100, pseudocount = 1) normalize(motif2) ## rowMeans ## Calculate motif rowMeans. rowMeans(motif) ## colMeans ## Calculate motif colMeans. colMeans(motif) ## colSums ## Calculate motif colSums colSums(motif) ## rowSums ## Calculate motif rowSums. rowSums(motif) ## nrow ## Count motif rows. nrow(motif) ## ncol ## Count motif columns. ncol(motif) ## colnames ## Get motif colnames. colnames(motif) ## rownames ## Get motif rownames. rownames(motif) ## cbind ## Bind motifs together to create a new motif. cbind(motif, motif2)