View source: R/map_ensembl_gene_id.R
map_ensembl_gene_id | R Documentation |
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.
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
)
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.
|
species |
ensembl_ids are mapped to |
ensembl_mapping_file |
path to the mappings tsv file |
mapped_df a data.frame of the provided ensembl_id's with mappings.
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()
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