AnnotateFeatures: AnnotateFeatures Annotate features in a Seurat object with...

In zh542370159/SCP: Single Cell Pipeline

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

Description

AnnotateFeatures 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 = 103,
  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	Name of the species to be used for annotation. Default is "Homo_sapiens".
IDtype	Type of identifier to use for annotation. Default is "symbol" with options "symbol", "ensembl_id", and "entrez_id".
db	Vector of database names to be used for annotation. Default is NULL.
db_update	Logical value indicating whether to update the database. Default is FALSE.
db_version	Version of the database to use. Default is "latest".
convert_species	A logical value indicating whether to use a species-converted database when the annotation is missing for the specified species. The default value is TRUE.
Ensembl_version	Version of the Ensembl database to use. Default is 103.
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	Logical value indicating whether to overwrite existing metadata. Default is FALSE.

See Also

PrepareDB ListDB

Examples

data("pancreas_sub")
pancreas_sub <- AnnotateFeatures(pancreas_sub,
  species = "Mus_musculus", IDtype = "symbol",
  db = c("Chromosome", "GeneType", "Enzyme", "TF", "CSPA", "VerSeDa")
)
head(pancreas_sub[["RNA"]]@meta.features)

## Annotate features using a GTF file
# pancreas_sub <- AnnotateFeatures(pancreas_sub, gtf = "/data/reference/CellRanger/refdata-gex-mm10-2020-A/genes/genes.gtf")
# head(pancreas_sub[["RNA"]]@meta.features)

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.