Add ArchR annotations to an ArchRProject

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")
)

Arguments

ArchRProj

An ArchRProject object.

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 ArchRAnno.

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 ArchRAnno file please select a valid collection from within that database.

name

The name of the peakAnnotation object to be stored in the ArchRProject.

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.