convert_motifs {universalmotif} | R Documentation |
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.
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.
Pagès H, Aboyoun P, Gentleman R, DebRoy S (2018). Biostrings: Efficient manipulation of biological strings. R package version 2.48.0.
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 }