map_ensembl_gene_id: Return mappings for Ensembl Gene IDs

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Return mappings for Ensembl Gene IDs

Description

Returns a data frame with the provided ensembl gene ids and requested mappings from biomaRt or a local file. If the mappings are absent from the local file, or the local file is not provided or missing, the mappings are retrieved by querying biomaRt.

Usage

map_ensembl_gene_id(
  ensembl_ids,
  mappings = c("ensembl_gene_id", "gene_biotype", "external_gene_name",
    "percentage_gene_gc_content"),
  species = getOption("scflow_species", default = "human"),
  ensembl_mapping_file = NULL
)

Arguments

ensembl_ids	vector of ensembl_ids, if versioned the version will be stripped.
mappings	the biomaRt attributes to be mapped or mappings file column names. ensembl_gene_id will be added if not included here. c("ensembl_gene_id", "external_gene_name")
species	ensembl_ids are mapped to human or mouse
ensembl_mapping_file	path to the mappings tsv file

Value

mapped_df a data.frame of the provided ensembl_id's with mappings.

See Also

Other annotation functions: .preprocess_seurat_object(), annotate_celltype_metrics(), annotate_integrated_sce(), annotate_merged_sce(), annotate_sce(), annotate_sce_cells(), annotate_sce_genes(), filter_sce(), find_cells(), find_singlets(), generate_sce(), merge_sce(), read_metadata(), report_celltype_metrics(), report_celltype_model(), report_merged_sce(), report_qc_sce(), run_doubletfinder(), sce_to_seu()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.