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apply groups to PlySummarizedExperiment

Source: R/dplyr-group_by.R
group_by.Rd

create grouping variables about the rowData and colData of a PlySummarizedExperiment object. Unlike the data.frame method the resulting output class is left unchanged. Thus dplyr generics for PlySummarizedExperiment must check grouping information manually.

Usage

# S3 method for class 'PlySummarizedExperiment'
group_by(.data, ..., .add = FALSE)

# S3 method for class 'PlySummarizedExperiment'
ungroup(x, ...)

Arguments

.data

An object Inheriting from PlySummarizedExperiment, the wrapper class for SummarizedExperiment objects

S4 Compatibility

At the moment, grouping on S4 Vectors is not yet supported. This is due to plyxp using [vec_group_loc][vctrs::vec_group_loc] to form grouping information. plyxp will eventually develop a method to handle S4 Vectors.

...

contextual expressions specifying which columns to ungroup. Omitting ... ungroups the entire object.

.add

When FALSE, the default, group_by() will override existing groups.

x

An object Inheriting from PlySummarizedExperiment, the wrapper class for SummarizedExperiment objects

Value

PlySummarizedExperiment object

Functions

  • ungroup(PlySummarizedExperiment): Ungroup a PlySummarizedExperiment object

Examples


group_by(se_simple, rows(direction), cols(condition))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> # Groups: rows(direction), cols(condition)
#>     .features .samples | counts logcounts | direction gene  length | condition
#>     <chr>     <chr>    |  <int>     <dbl> | <chr>     <chr>  <int> | <chr>    
#>   1 row_1     col_1    |     14      2.64 | -         g1         1 | cntrl    
#>   2 row_2     col_1    |     19      2.94 | +         g2        24 | cntrl    
#>   3 row_3     col_1    |     16      2.77 | +         g3        60 | cntrl    
#>   4 row_4     col_1    |     11      2.40 | -         g4        39 | cntrl    
#>   5 row_5     col_1    |     18      2.89 | +         g5        37 | cntrl    
#>   …   …         …             …        …    …          …         …     …      
#> n-4 row_1     col_4    |      9      2.20 | -         g1         1 | drug     
#> n-3 row_2     col_4    |      4      1.39 | +         g2        24 | drug     
#> n-2 row_3     col_4    |     20      3.00 | +         g3        60 | drug     
#> n-1 row_4     col_4    |      3      1.10 | -         g4        39 | drug     
#> n   row_5     col_4    |      5      1.61 | +         g5        37 | drug     
#> # ℹ n = 20
#> # ℹ 1 more variable: sample <chr>