Create a genome annotation object for ArchR

This function will create a genome annotation object that can be used for creating ArrowFiles or an ArchRProject, etc.

createGenomeAnnotation(
  genome = NULL,
  chromSizes = NULL,
  blacklist = NULL,
  filter = TRUE,
  filterChr = c("chrM")
)

Arguments

genome

Either (i) a string that is a valid BSgenome or (ii) a BSgenome object (ie "hg38" or "BSgenome.Hsapiens.UCSC.hg38").

chromSizes

A GRanges object containing chromosome start and end coordinates.

blacklist

A GRanges object containing regions that should be excluded from analyses due to unwanted biases.

filter

A boolean value indicating whether non-standard chromosome scaffolds should be excluded. These "non-standard" chromosomes are defined by filterChrGR().

filterChr

A character vector indicating the seqlevels that should be removed if manual removal is desired for certain seqlevels. If no manual removal is desired, filterChr should be set to NULL.