Create a gene annotation object for ArchR — createGeneAnnotation • ArchR

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

createGeneAnnotation(
  genome = NULL,
  TxDb = NULL,
  OrgDb = NULL,
  genes = NULL,
  exons = NULL,
  TSS = NULL,
  annoStyle = NULL
)

Arguments

genome	A string that specifies the genome (ie "hg38", "hg19", "mm10", "mm9"). If `genome` is not supplied, `TxDb` and `OrgDb` are required. If genome is supplied, `TxDb` and `OrgDb` will be ignored.
TxDb	A `TxDb` object (transcript database) from Bioconductor which contains information for gene/transcript coordinates. For example, from `txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene`.
OrgDb	An `OrgDb` object (organism database) from Bioconductor which contains information for gene/transcript symbols from ids. For example, from `orgdb <- org.Hs.eg.db`.
genes	A `GRanges` object containing gene coordinates (start to end). Must have a symbols column matching the symbols column of `exons`.
exons	A `GRanges` object containing gene exon coordinates. Must have a symbols column matching the symbols column of `genes`.
TSS	A `GRanges` object containing standed transcription start site coordinates for computing TSS enrichment scores downstream.
annoStyle	annotation style to map between gene names and various gene identifiers e.g. "ENTREZID", "ENSEMBL".