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: Features=63677 | Samples=8 | 
#> #   Assays=counts
#> #                                 |----------------- COVARIATES ---------------|
#>        .feature  .sample | counts | SampleName cell  dex   albut Run   avgLength
#>        <chr>     <chr>   | <chr>  | <fct>      <fct> <fct> <fct> <fct> <chr>    
#> 1      ENSG0000… SRR103… | 679    | GSM1275862 N613… untrt untrt SRR1… 126      
#> 2      ENSG0000… SRR103… | 0      | GSM1275862 N613… untrt untrt SRR1… 126      
#> 3      ENSG0000… SRR103… | 467    | GSM1275862 N613… untrt untrt SRR1… 126      
#> 4      ENSG0000… SRR103… | 260    | GSM1275862 N613… untrt untrt SRR1… 126      
#> 5      ENSG0000… SRR103… | 60     | GSM1275862 N613… untrt untrt SRR1… 126      
#>        --------  ------- - ------ - ---------- ----  ---   ----- ---   ---------
#> 509412 ENSG0000… SRR103… | 0      | GSM1275875 N061… trt   untrt SRR1… 98       
#> 509413 ENSG0000… SRR103… | 0      | GSM1275875 N061… trt   untrt SRR1… 98       
#> 509414 ENSG0000… SRR103… | 0      | GSM1275875 N061… trt   untrt SRR1… 98       
#> 509415 ENSG0000… SRR103… | 0      | GSM1275875 N061… trt   untrt SRR1… 98       
#> 509416 ENSG0000… SRR103… | 0      | GSM1275875 N061… trt   untrt SRR1… 98       
#> # ℹ 16 more variables: Experiment <fct>, Sample <fct>, BioSample <fct>,
#> #   condition <fct>, `|` <|>, gene_id <chr>, gene_name <chr>, entrezid <chr>,
#> #   gene_biotype <chr>, gene_seq_start <chr>, gene_seq_end <chr>,
#> #   seq_name <chr>, seq_strand <chr>, seq_coord_system <chr>, symbol <chr>,
#> #   description <chr>