gene_id_type {scPipe} | R Documentation

## 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)

[Package scPipe version 1.6.0 Index]