If the source was set to
addTFBS, the argument
nCores is ignored.
overlapPeaksAndTFBS(GRN, nCores = 2, forceRerun = FALSE, ...)
Object of class
Integer >0. Default 1. Number of cores to use.
A value >1 requires the
BiocParallel package (as it is listed under
Suggests, it may not be installed yet).
FALSE. Force execution, even if the GRN object already contains the result. Overwrites the old results.
No default. Only relevant if
source = "JASPAR" has been selected in
addTFBS, ignored otherwise. Additional arguments for
motifmatchr::matchMotifs such as custom background nucleotide frequencies or p-value cutoffs. For more information, type
GRN object, with added data from this function (
GRN@data$TFs$TF_peak_overlap in particular)
# See the Workflow vignette on the GRaNIE website for examples GRN = loadExampleObject() #> Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds #> Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing! GRN = overlapPeaksAndTFBS(GRN, nCores = 2, forceRerun = FALSE) #> INFO [2023-03-06 16:40:12] Data already exists in object. Set forceRerun = TRUE to regenerate and overwrite. #> INFO [2023-03-06 16:40:12] Finished successfully. Execution time: 0 secs