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' x[i] ## S4 replacement method for signature 'universalmotif' x[i] <- value ## S4 method for signature 'universalmotif' initialize(.Object, name, altname, family, organism, motif, alphabet = "DNA", type, icscore, nsites, pseudocount = 1, bkg, bkgsites, consensus, strand = "+-", pval, qval, eval, multifreq, extrainfo, gapinfo) ## 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 |
|
gapinfo |
|
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
0-order probabilities must be provided for all letters.
bkgsites
numeric(1)
consensus
character
Generated automatically.
strand
character(1)
pval
numeric(1)
qval
numeric(1)
eval
numeric(1)
multifreq
list
extrainfo
character
gapinfo
universalmotif_gapped(1)
Benjamin Jean-Marie Tremblay, benjamin.tremblay@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)