Annotate Features

Annotate features in a Seurat object with additional metadata from databases or a GTF file.

Usage

AnnotateFeatures(
  srt,
  species = "Homo_sapiens",
  IDtype = c("symbol", "ensembl_id", "entrez_id"),
  db = NULL,
  db_update = FALSE,
  db_version = "latest",
  convert_species = TRUE,
  Ensembl_version = NULL,
  mirror = NULL,
  gtf = NULL,
  merge_gtf_by = "gene_name",
  columns = c("seqname", "feature", "start", "end", "strand", "gene_id", "gene_name",
    "gene_type"),
  assays = "RNA",
  overwrite = FALSE
)

Arguments

srt: Seurat object to be annotated.
species: A character vector specifying the species for which the gene annotation databases should be prepared. Can be "Homo_sapiens" or "Mus_musculus".
IDtype: Type of identifier to use for annotation. Options are "symbol", "ensembl_id", or "entrez_id". Default is "symbol".
db: A character vector specifying the annotation sources to be included in the gene annotation databases. Can be one or more of "GO", "GO_BP", "GO_CC", "GO_MF", "KEGG", "WikiPathway", "Reactome", "CORUM", "MP", "DO", "HPO", "PFAM", "CSPA", "Surfaceome", "SPRomeDB", "VerSeDa", "TFLink", "hTFtarget", "TRRUST", "JASPAR", "ENCODE", "MSigDB", "CellTalk", "CellChat", "Chromosome", "GeneType", "Enzyme", "TF".
db_update: Whether the gene annotation databases should be forcefully updated. If set to FALSE, the function will attempt to load the cached databases instead. Default is FALSE.
db_version: A character vector specifying the version of the gene annotation databases to be retrieved. Default is "latest".
convert_species: Whether to use a species-converted database when the annotation is missing for the specified species. Default is TRUE.
Ensembl_version: An integer specifying the Ensembl version. Default is NULL. If NULL, the latest version will be used.
mirror: URL of the mirror to use for Ensembl database. Default is NULL.
gtf: Path to the GTF file to be used for annotation. Default is NULL.
merge_gtf_by: Column name to merge the GTF file by. Default is "gene_name".
columns: Vector of column names to be used from the GTF file. Default is "seqname", "feature", "start", "end", "strand", "gene_id", "gene_name", "gene_type".
assays: Character vector of assay names to be annotated. Default is "RNA".
overwrite: Whether to overwrite existing metadata. Default is FALSE.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- AnnotateFeatures(
  pancreas_sub,
  species = "Mus_musculus",
  db = c(
    "Chromosome",
    "GeneType",
    "Enzyme",
    "TF",
    "CSPA",
    "VerSeDa"
  )
)
head(
  GetFeaturesData(
    pancreas_sub
  )
)

# Annotate features using a GTF file
pancreas_sub <- AnnotateFeatures(
  pancreas_sub,
  gtf = "/refdata-gex-mm10-2020-A/genes/genes.gtf"
)
head(
  GetFeaturesData(
    pancreas_sub
  )
)
} # }

Usage

Arguments

See also

Examples