Create a genome annotation object for ArchR — createGenomeAnnotation • 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`.