universalmotif-class: universalmotif: Motif class.
In universalmotif: Import, Modify, and Export Motifs with R

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.

## 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`	`character` Slot.
`value`	Object to replace slot with.
`.Object`	universalmotif Final motif.
`name`	`character(1)` Motif name.
`altname`	`character(1)` Alternate motif name.
`family`	`character(1)` Transcription factor family.
`organism`	`character(1)` Species of origin.
`motif`	`matrix` Each column represents a position in the motif.
`alphabet`	`character(1)` One of `c('DNA', 'RNA', 'AA')`, or a combined string representing the letters.
`type`	`character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`.
`icscore`	`numeric(1)` Total information content. Automatically generated.
`nsites`	`numeric(1)` Number of sites the motif was constructed from.
`pseudocount`	`numeric(1)` Correction to be applied to prevent `-Inf` from appearing in PWM matrices.
`bkg`	`numeric` A vector of probabilities, each between 0 and 1. If higher order backgrounds are provided, then the elements of the vector must be named.
`bkgsites`	`numeric(1)` Total number of sites used to find the motif.
`consensus`	`character(1)` Consensus string. Automatically generated for 'DNA', 'RNA', and 'AA' alphabets.
`strand`	`character(1)` Whether the motif is specific to a certain strand.
`pval`	`numeric(1)` P-value associated with motif.
`qval`	`numeric(1)` Adjusted P-value associated with motif.
`eval`	`numeric(1)` E-value associated with motif.
`multifreq`	`list` See `add_multifreq()`.
`extrainfo`	`character` Any other extra information, represented as a named character vector.
`gapinfo`	`universalmotif_gapped(1)` Gapped motif information.
`object`	universalmotif Motif.
`select`	`numeric` Columns to keep.
`...`	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

## [
## 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)