convert_motifs {universalmotif} | R Documentation |
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.
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")
motifs |
Single motif object or list. See details. |
class |
|
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
Single motif object or list.
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.
Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca
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.
# 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 }