Add motif annotations to an ArchRProject — addMotifAnnotations • ArchR

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",
  name = "Motif",
  species = NULL,
  collection = "CORE",
  motifPWMs = NULL,
  cutOff = 5e-05,
  width = 7,
  version = 2,
  force = FALSE,
  logFile = createLogFile("addMotifAnnotations"),
  ...
)

Arguments

ArchRProj	An `ArchRProject` object.
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 or (ii) one of "cisbp", "encode", or "homer" which gives the corresponding motif sets from the `chromVAR` package.
name	The name of the `peakAnnotation` object to be stored in the provided `ArchRProject`
species	The name of the species relevant to the supplied `ArchRProject`. This is used for identifying which motif to be used from CisBP/JASPAR. By default, this function will attempt to guess the species based on the value from `getGenome()`.
collection	If one of the JASPAR motif sets is used via `motifSet`, this parameter allows you to indicate the JASPAR collection to be used. See `getMatrixSet()` from `TFBSTools` for all options to supply for collection.
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 `MOODS` for more details on this determination).
width	The width in basepairs to consider for motif matches. See the `motimatchr` package for more information.
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 `peakAnnotation` object indicated by `name` to be overwritten if it already exists in the given `ArchRProject`.
logFile	The path to a file to be used for logging ArchR output.
...	Additional parameters to be passed to `TFBSTools::getMatrixSet` for getting a PWM object.