Description Usage Arguments Value Slots Author(s) Examples
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
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 | ## 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, b2tremblay@uwaterloo.ca
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 | ## [
## 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.