gene_id_type: Get or set 'gene_id_type' from a SingleCellExperiment object

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

Get or set gene_id_type from a SingleCellExperiment object

Description

Get or set gene_id_type from a SingleCellExperiment object

Usage

gene_id_type(object)

gene_id_type(object) <- value

gene_id_type.sce(object)

## S4 method for signature 'SingleCellExperiment'
gene_id_type(object)

## S4 replacement method for signature 'SingleCellExperiment'
gene_id_type(object) <- value

Arguments

object	A SingleCellExperiment object.
value	Value to be assigned to corresponding object.

Value

the gene id type used by Biomart

gene id type string

Author(s)

Luyi Tian

Examples

data("sc_sample_data")
data("sc_sample_qc")
sce = SingleCellExperiment(assays = list(counts = as.matrix(sc_sample_data)))
organism(sce) = "mmusculus_gene_ensembl"
gene_id_type(sce) = "ensembl_gene_id"
QC_metrics(sce) = sc_sample_qc
demultiplex_info(sce) = cell_barcode_matching
UMI_dup_info(sce) = UMI_duplication

gene_id_type(sce)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.