addArchRAnnotations | R Documentation |
This function adds information about which peaks in the ArchR database contain input regions to a given ArchRProject. For each peak, a binary value is stored indicating whether each region is observed within the peak region.
addArchRAnnotations(
ArchRProj = NULL,
db = "ArchR",
collection = "EncodeTFBS",
name = collection,
force = FALSE,
logFile = createLogFile("addArchRAnnotations")
)
ArchRProj |
An |
db |
A string indicating the database or a path to a database to use for peak annotation. Options include ArchR,
LOLA, and a valid path to a file of class |
collection |
A string indicating which collection within the database to collect for annotation.
For ArchR, options are "ATAC", "EncodeTFBS", "CistromeTFBS", or "Codex".
For LOLA, options include "EncodeTFBS" "CistromeTFBS", "CistromeEpigenome", "Codex", or "SheffieldDnase".
If supplying a custom |
name |
The name of the |
force |
A boolean value indicating whether to force the |
logFile |
The path to a file to be used for logging ArchR output. |
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