GRN
objectoverlapPeaksAndTFBS.Rd
If the source was set to JASPAR
in addTFBS
, the argument nCores
is ignored.
overlapPeaksAndTFBS(GRN, nCores = 2, forceRerun = FALSE, ...)
Object of class GRN
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).
TRUE
or FALSE
. Default 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 ?motifmatchr::matchMotifs
An updated 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 [2024-09-25 19:18:22] Data already exists in object or the specified file already exists. Set forceRerun = TRUE to regenerate and overwrite.
#> INFO [2024-09-25 19:18:22] Finished successfully. Execution time: 0 secs