Un-normalized count data for mouse retina RNA-seq samples

gene_expression() returns gene-level raw expression counts from the spaceflight and ground-based experiment involving mouse retina samples.

Usage

gene_expression(format = c("long", "wide"), only_expressed_genes = FALSE)

Source

doi:10.26030/d6dj-d777

Arguments

format: A string indicating the format of the returned object. Must be one of: "long" (default): a tibble with one row per gene × sample combination. "wide": a numeric matrix of counts with genes as rows and sample IDs as columns — suitable for downstream differential expression analysis.
only_expressed_genes: Logical. If TRUE, filters out genes that have zero counts in all samples. Default is FALSE.

Value

Long format:

A tibble with columns:

sample_id: Character. Unique sample identifier matching those in samples().
ensembl_gen_id: Character. Ensembl gene ID (e.g., ENSMUSG00000000001).
gene_symbol: Gene symbol (e.g., Gnai3), provided for convenience.
counts: Integer. Raw expression counts for that gene in that sample.

Wide format:

A numeric matrix. Rows correspond to genes (named by ensembl_gen_id), columns to samples (column names are sample_ids). Expression values are raw un-normalized counts.

Details

The dataset comprises 35 samples and expression counts for ~57,000 genes (Ensembl IDs).

Examples

# Un-normalized counts in long format
gene_expression()
#> # A tibble: 1,989,400 × 4
#>    sample_id           ensembl_gen_id     gene_symbol counts
#>    <chr>               <chr>              <chr>        <int>
#>  1 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000001 Gnai3         2132
#>  2 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000003 Pbsn             0
#>  3 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000028 Cdc45          109
#>  4 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000031 H19             29
#>  5 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000037 Scml2           92
#>  6 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000049 Apoh            22
#>  7 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000056 Narf          3614
#>  8 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000058 Cav2          3464
#>  9 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000078 Klf6          2464
#> 10 MHU-8_RTN_FLT_FLT02 ENSMUSG00000000085 Scmh1         2779
#> # ℹ 1,989,390 more rows

# Un-normalized counts in wide format (matrix)
gene_expression("wide")[1:5, 1:3]
#>                    MHU-8_RTN_FLT_FLT02 MHU-8_RTN_FLT_FLT03 MHU-8_RTN_FLT_FLT04
#> ENSMUSG00000000001                2132                2501                1979
#> ENSMUSG00000000003                   0                   0                   0
#> ENSMUSG00000000028                 109                 125                 142
#> ENSMUSG00000000031                  29                  27                  28
#> ENSMUSG00000000037                  92                 129                  90