Get the globally defined genome, the geneAnnotation, or genomeAnnotation objects associated with the globally defined genome.

This function will retrieve the genome that is currently in use by ArchR. Alternatively, this function can return either the geneAnnotation or the genomeAnnotation associated with the globally defined genome if desired.

getArchRGenome(geneAnnotation = FALSE, genomeAnnotation = FALSE)

Arguments

geneAnnotation

A boolean value indicating whether the geneAnnotation associated with the ArchRGenome should be returned instead of the globally defined genome. The geneAnnotation is used downstream to calculate things like TSS Enrichment Scores. This function is not meant to be run with both geneAnnotation and genomeAnnotation set to TRUE (it is an either/or return value).

genomeAnnotation

A boolean value indicating whether the genomeAnnotation associated with the ArchRGenome should be returned instead of the globally defined genome. The genomeAnnotation is used downstream to determine things like chromosome sizes and nucleotide content. This function is not meant to be run with both geneAnnotation and genomeAnnotation set to TRUE (it is an either/or return value).