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Annotate Features

Source: R/AnnotateFeatures.R
AnnotateFeatures.Rd

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,
  ...,
  verbose = TRUE
)

Arguments

srt

Seurat object to be annotated.

species

"Homo_sapiens" or "Mus_musculus".

IDtype

Type of identifier to use for annotation. Options are "symbol", "ensembl_id", or "entrez_id".

db

Annotation sources. 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", "CytoTRACE2". MSigDB subcollections use "MSigDB_<collection>" (e.g. "MSigDB_H"). "CytoTRACE2" is species-independent and is required by RunCytoTRACE.

db_update

Force a refresh. FALSE loads the cache when available.

db_version

Database version to retrieve.

convert_species

Use a species-converted database when the annotation is missing for species.

Ensembl_version

Ensembl version. NULL uses the latest.

mirror

URL of the mirror to use for Ensembl database.

gtf

Path to the GTF file to be used for annotation.

merge_gtf_by

Column name to merge the GTF file by.

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.

overwrite

Whether to overwrite existing metadata.

...

Passed to helper functions.

verbose

Whether to print the message. Default is TRUE.

See also

PrepareDB, ListDB

Examples

data(pancreas_sub)
pancreas_sub <- AnnotateFeatures(
  pancreas_sub,
  species = "Mus_musculus",
  db = "TF"
)
#> ℹ [2026-08-30 04:00:30] Species: "Mus_musculus"
#> ℹ [2026-08-30 04:00:30] Preparing database: TF
head(
  GetFeaturesData(
    pancreas_sub
  )
)
#>               highly_variable_genes   TF
#> Xkr4                          False <NA>
#> Mrpl15                        False <NA>
#> Npbwr1                         <NA> <NA>
#> 4732440D04Rik                 False <NA>
#> Gm26901                       False <NA>
#> Sntg1                          True <NA>

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