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",
  annoName = "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 name of a curated 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 chromVAR package, or (iii) "vierstra" which gives the clustered archetype motifs created by Jeff Vierstra (https://github.com/jvierstra/motif-clustering).
annoName: The name of the peakAnnotation object to be stored in the provided ArchRProject
species: The latin name of the species relevant to the supplied ArchRProject. This is used for identifying which motif to be used from CisBP/JASPAR. For JASPAR, species is passed to TFBS::getMatrixSet and some species names are not recognized. In these cases it is possible to use the NCBI taxonomy ID. 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. If motifSet is "vierstra", then this must either be "archetype" (for the v2.1 clustered models) or "individual" (for the original v1 individual motif models). NOTE: vierstra archetype motifs are currently in beta and have not been finalized by Jeff Vierstra.
motifPWMs: A custom set of motif PWMs as a PWMatrixList to be used instead of motifSet for adding motif annotations. If motifPWMs is used, motifSet will be ignored.
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 annoName 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 JASPAR PWM object.

Examples


# Get Test ArchR Project
proj <- getTestProject()

# Add Motif Annotations
proj <- addMotifAnnotations(proj, motifSet = "cisbptest", annoName = "test")