convert_geneid {scPipe} | R Documentation

## convert the gene ids of a SingleCellExperiment object

### Description

convert the gene ids of a SingleCellExperiment object

### Usage

    convert_geneid(sce, returns = "external_gene_name", all = TRUE)

### Arguments

`sce` | a SingleCellExperiment object
`returns` | the gene id which is set as return. Default to be 'external_gene_name' A possible list of attributes can be retrieved using the function `listAttributes` from `biomaRt` package. The commonly used id types are 'external_gene_name', 'ensembl_gene_id' or 'entrezgene'.
`all` | logic. For genes that cannot covert to new gene id, keep them with the old id or delete them. The default is keep them.

### Details

convert the gene id of all datas in the SingleCellExperiment object

### Value

sce with converted id

### Examples

    # the gene id in example data are `external_gene_name`
    # the following example will convert it to `external_gene_name`.
    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
    head(rownames(sce))
    sce = convert_geneid(sce, return="external_gene_name")
    head(rownames(sce))

[Package scPipe version 1.4.1 Index]