View source: R/AnnotationPeaks.R
addMotifAnnotations | R Documentation |
This function adds information about which peaks contain motifs to a given ArchRProject. For each peak, a binary value is stored indicating whether each motif is observed within the peak region.
addMotifAnnotations(
ArchRProj = NULL,
motifSet = "cisbp",
annoName = "Motif",
species = NULL,
collection = "CORE",
motifPWMs = NULL,
cutOff = 5e-05,
width = 7,
version = 2,
force = FALSE,
logFile = createLogFile("addMotifAnnotations"),
...
)
ArchRProj |
An |
motifSet |
The motif set to be used for annotation. Options include: (i) "JASPAR2016", "JASPAR2018", "JASPAR2020"
which gives the 2016, 2018 or 2020 version of JASPAR motifs, (ii) one of "cisbp", "encode", or "homer" which gives the
corresponding motif sets from the |
annoName |
The name of the |
species |
The name of the species relevant to the supplied |
collection |
If one of the JASPAR motif sets is used via |
motifPWMs |
A custom set of motif PWMs as a PWMList for adding motif annotations. |
cutOff |
The p-value cutoff to be used for motif search. The p-value is determined vs a background set of sequences
(see |
width |
The width in basepairs to consider for motif matches. See the |
version |
An integer specifying version 1 or version 2 of chromVARmotifs see github for more info GreenleafLab/chromVARmotifs. |
force |
A boolean value indicating whether to force the |
logFile |
The path to a file to be used for logging ArchR output. |
... |
Additional parameters to be passed to |
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