Get DESCRIPTION from gene SYMBOL for Human and Mouse

describe_transcript

describe_transcript(.data)

.describe_transcript_SE(.data)

# S4 method for class 'SummarizedExperiment'
describe_transcript(.data)

# S4 method for class 'RangedSummarizedExperiment'
describe_transcript(.data)

Arguments

.data: A tt or tbl object.

Value

A tbl

A `SummarizedExperiment` object

A consistent object (to the input) including additional columns for transcript symbol

References

Mangiola, S., Molania, R., Dong, R., Doyle, M. A., & Papenfuss, A. T. (2021). tidybulk: an R tidy framework for modular transcriptomic data analysis. Genome Biology, 22(1), 42. doi:10.1186/s13059-020-02233-7

Carlson, M. (2019). org.Hs.eg.db: Genome wide annotation for Human. R package version 3.8.2.

Carlson, M. (2019). org.Mm.eg.db: Genome wide annotation for Mouse. R package version 3.8.2.

Examples

## Load airway dataset for examples

  data('airway', package = 'airway')
  # Ensure a 'condition' column exists for examples expecting it

    SummarizedExperiment::colData(airway)$condition <- SummarizedExperiment::colData(airway)$dex



describe_transcript(airway)
#> # A SummarizedExperiment-tibble abstraction: 509,416 × 25
#> # Features=63677 | Samples=8 | Assays=counts
#>    .feature        .sample   counts SampleName cell  dex   albut Run   avgLength
#>    <chr>           <chr>      <int> <fct>      <fct> <fct> <fct> <fct>     <int>
#>  1 ENSG00000000003 SRR10395…    679 GSM1275862 N613… untrt untrt SRR1…       126
#>  2 ENSG00000000005 SRR10395…      0 GSM1275862 N613… untrt untrt SRR1…       126
#>  3 ENSG00000000419 SRR10395…    467 GSM1275862 N613… untrt untrt SRR1…       126
#>  4 ENSG00000000457 SRR10395…    260 GSM1275862 N613… untrt untrt SRR1…       126
#>  5 ENSG00000000460 SRR10395…     60 GSM1275862 N613… untrt untrt SRR1…       126
#>  6 ENSG00000000938 SRR10395…      0 GSM1275862 N613… untrt untrt SRR1…       126
#>  7 ENSG00000000971 SRR10395…   3251 GSM1275862 N613… untrt untrt SRR1…       126
#>  8 ENSG00000001036 SRR10395…   1433 GSM1275862 N613… untrt untrt SRR1…       126
#>  9 ENSG00000001084 SRR10395…    519 GSM1275862 N613… untrt untrt SRR1…       126
#> 10 ENSG00000001167 SRR10395…    394 GSM1275862 N613… untrt untrt SRR1…       126
#> # ℹ 40 more rows
#> # ℹ 16 more variables: Experiment <fct>, Sample <fct>, BioSample <fct>,
#> #   condition <fct>, gene_id <chr>, gene_name <chr>, entrezid <int>,
#> #   gene_biotype <chr>, gene_seq_start <int>, gene_seq_end <int>,
#> #   seq_name <chr>, seq_strand <int>, seq_coord_system <int>, symbol <chr>,
#> #   description <lgl>, GRangesList <list>