Convert motif class.

Description

Allows for easy transfer of motif information between different classes 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 needed to convert 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

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, b2tremblay@uwaterloo.ca

References

Bembom O (2018). seqLogo: Sequence logos for DNA sequence alignments. R package version 1.46.0.

Droit A, Gottardo R, Robertson G, Li L (2014). rGADEM: de novo motif discovery. R package version 2.28.0.

Mercier E, Gottardo R (2014). MotIV: Motif Identification and Validation. R package version 1.36.0.

Ou J, Wolfe SA, Brodsky MH, Zhu LJ (2018). “motifStack for the analysis of transcription factor binding site evolution.” Nature Methods, 15, 8-9. doi: 10.1038/nmeth.4555, http://dx.doi.org/10.1038/nmeth.4555.

Shannon P, Richards M (2018). MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs. R package version 1.22.0.

Stojnic R, Diez D (2015). PWMEnrich: PWM enrichment analysis. R package version 4.16.0.

Tan G, Lenhard B (2016). “TFBSTools: an R/Bioconductor package for transcription factor binding site analysis.” Bioinformatics, 32, 1555-1556. doi: 10.1093/bioinformatics/btw024, http://bioinformatics.oxfordjournals.org/content/32/10/1555.

Yao Z (2012). motifRG: A package for discriminative motif discovery, designed for high throughput sequencing dataset. R package version 1.24.0.

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
}