universalmotif-class: universalmotif: Motif class.

Description Usage Arguments Value Slots Author(s) Examples

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

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## 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, b2tremblay@uwaterloo.ca

Examples

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## [
## 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)

universalmotif documentation built on April 8, 2021, 6 p.m.