convert_motifs: Convert motif class.

In universalmotif: Import, Modify, and Export Motifs with R

Description

Allows for easy transfer of motif information between different classes as defined by other Bioconductor packages. This function is also used by nearly all other functions in this package, so any motifs of a compatible class can be used without needing to be converted beforehand.

Usage

convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'list'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'universalmotif'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'MotifList'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'TFFMFirst'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PFMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PWMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'ICMatrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'XMatrixList'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pwm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pcm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'pfm'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'PWM'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'Motif'
convert_motifs(motifs, class = "universalmotif-universalmotif")

## S4 method for signature 'matrix'
convert_motifs(motifs, class = "universalmotif-universalmotif")

Arguments

motifs	Single motif object or list. See details.
class	character(1) Desired motif class. Input as 'package-class'. If left empty, defaults to 'universalmotif-universalmotif'. (See details.)

Details

The following packge-class combinations can be used as input:

• MotifDb-MotifList

• TFBSTools-PFMatrix

• TFBSTools-PWMatrix

• TFBSTools-ICMatrix

• TFBSTools-PFMatrixList

• TFBSTools-PWMatrixList

• TFBSTools-ICMatrixList

• TFBSTools-TFFMFirst

• seqLogo-pwm

• motifStack-pcm

• motifStack-pfm

• PWMEnrich-PWM

• motifRG-Motif

• universalmotif-universalmotif

• matrix

The following package-class combinations can be output:

• MotIV-pwm2

• TFBSTools-PFMatrix

• TFBSTools-PWMatrix

• TFBSTools-ICMatrix

• TFBSTools-TFFMFirst

• seqLogo-pwm

• motifStack-pcm

• motifStack-pfm

• PWMEnrich-PWM

• Biostrings-PWM (type = 'log2prob')

• rGADEM-motif

• universalmotif-universalmotif

Value

Single motif object or list.

Methods (by class)

• list: Convert a list of motifs.

• universalmotif: Convert a universalmotif object.

• MotifList: Convert MotifList motifs. (MotifDb)

• TFFMFirst: Convert TFFMFirst motifs. (TFBSTools)

• PFMatrix: Convert PFMatrix motifs. (TFBSTools)

• PWMatrix: Convert PWMatrix motifs. (TFBSTools)

• ICMatrix: Convert ICMatrix motifs. (TFBSTools)

• XMatrixList: Convert XMatrixList motifs. (TFBSTools)

• pwm: Convert pwm motifs. (seqLogo)

• pcm: Convert pcm motifs. (motifStack)

• pfm: Convert pfm motifs. (motifStack)

• PWM: Convert PWM motifs. (PWMEnrich)

• Motif: Convert Motif motifs. (motifRG)

• matrix: Create motif from matrices.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

References

\insertRef

seqlogouniversalmotif

\insertRef

rgademuniversalmotif

\insertRef

motivuniversalmotif

\insertRef

motifstackuniversalmotif

\insertRef

motifdbuniversalmotif

\insertRef

pwmenrichuniversalmotif

\insertRef

tfbstoolsuniversalmotif

\insertRef

motifrguniversalmotif

Examples

# Convert from universalmotif:
jaspar <- read_jaspar(system.file("extdata", "jaspar.txt",
                                  package = "universalmotif"))
if (requireNamespace("motifStack", quietly = TRUE)) {
  jaspar.motifstack.pfm <- convert_motifs(jaspar, "motifStack-pfm")
}

# Convert from another class to universalmotif:
if (requireNamespace("TFBSTools", quietly = TRUE)) {
library(TFBSTools)
data(MA0003.2)
motif <- convert_motifs(MA0003.2)

# Convert from another class to another class
if (requireNamespace("PWMEnrich", quietly = TRUE)) {
  motif <- convert_motifs(MA0003.2, "PWMEnrich-PWM")
}

# The 'convert_motifs' function is embedded in the rest of the universalmotif
# functions: non-universalmotif class motifs can be used
MA0003.2.trimmed <- trim_motifs(MA0003.2)
# Note: if the motif object going in has information that the
# 'universalmotif' class can't hold, it will be lost
}

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