Append samples from multiple SummarizedExperiment objects

Source: R/dplyr_methods.R

Append samples from multiple SummarizedExperiment objects by column-binding them. This function is equivalent to cbind but provides a tidyverse-like interface.

# S3 method for class 'SummarizedExperiment'
append_samples(x, ..., .id = NULL)

Arguments

x

First SummarizedExperiment object to combine

...

Additional SummarizedExperiment objects to combine by samples

.id

Object identifier (currently not used)

Value

A combined SummarizedExperiment object

References

Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2

Examples

data(se)
append_samples(se, se)
#> ! tidySummarizedExperiment says: you have duplicated sample names, they will be made unique.
#> Warning: you have duplicated sample names, they will be made unique.
#> # A SummarizedExperiment-tibble abstraction: Features=100 | Samples=16 | 
#> #   Assays=counts
#> #                                 |----------------- COVARIATES ---------------|
#>      .feature    .sample | counts | SampleName cell  dex   albut Run   avgLength
#>      <chr>       <chr>   | <chr>  | <fct>      <fct> <fct> <fct> <fct> <chr>    
#> 1    LRG_239     SRR103… | 0      | GSM1275862 N613… untrt untrt SRR1… 126      
#> 2    ENSG000002… SRR103… | 0      | GSM1275862 N613… untrt untrt SRR1… 126      
#> 3    ENSG000001… SRR103… | 0      | GSM1275862 N613… untrt untrt SRR1… 126      
#> 4    ENSG000002… SRR103… | 0      | GSM1275862 N613… untrt untrt SRR1… 126      
#> 5    ENSG000002… SRR103… | 0      | GSM1275862 N613… untrt untrt SRR1… 126      
#>      --------    ------- - ------ - ---------- ----  ---   ----- ---   ---------
#> 1596 ENSG000001… SRR103… | 338    | GSM1275875 N061… trt   untrt SRR1… 98       
#> 1597 ENSG000002… SRR103… | 0      | GSM1275875 N061… trt   untrt SRR1… 98       
#> 1598 ENSG000002… SRR103… | 11     | GSM1275875 N061… trt   untrt SRR1… 98       
#> 1599 ENSG000001… SRR103… | 0      | GSM1275875 N061… trt   untrt SRR1… 98       
#> 1600 ENSG000001… SRR103… | 53     | GSM1275875 N061… trt   untrt SRR1… 98       
#> # ℹ 5 more variables: Experiment <fct>, Sample <fct>, BioSample <fct>, `|` <|>,
#> #   bla <chr>