universalmotif-class {universalmotif}

R Documentation

universalmotif: Motif class.

Description

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.

Usage

## 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)

Arguments

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.

Value

A motif object of class universalmotif.

Slots

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)

Author(s)

Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca

Examples

## [
## 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)

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