Contextual user-facing helper function for dplyr verbs with SummarizedExperiment
objects. These functions are intended to be used as the top level call to
any dplyr verbs ...
argument, similar to that of across()
/if_any()
/if_all()
.
Specifies that the following expressions should be evaluated within the colData context.
Specifies that the following expressions should be evaluated within the rowData context.
Specify a single expression to evaluate in another context
Specify a single expression to evaluate in another context
Specify a single expression to evaluate in another context
Usage
cols(...)
rows(...)
col_ctx(x, asis = FALSE)
row_ctx(x, asis = FALSE)
assay_ctx(x, asis = FALSE)
Examples
# cols
mutate(se_simple,
cols(is_drug = condition=="drug"),
#bind a different context
effect = col_ctx(counts + (is_drug * rbinom(n(), 20, .3))))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | counts logcounts effect | gene length direction |
#> <chr> <chr> | <int> <dbl> <int> | <chr> <int> <chr> |
#> 1 row_1 col_1 | 14 2.64 14 | g1 1 - |
#> 2 row_2 col_1 | 19 2.94 19 | g2 24 + |
#> 3 row_3 col_1 | 16 2.77 16 | g3 60 + |
#> 4 row_4 col_1 | 11 2.40 11 | g4 39 - |
#> 5 row_5 col_1 | 18 2.89 18 | g5 37 + |
#> … … … … … … … … …
#> n-4 row_1 col_4 | 9 2.20 13 | g1 1 - |
#> n-3 row_2 col_4 | 4 1.39 9 | g2 24 + |
#> n-2 row_3 col_4 | 20 3.00 23 | g3 60 + |
#> n-1 row_4 col_4 | 3 1.10 8 | g4 39 - |
#> n row_5 col_4 | 5 1.61 15 | g5 37 + |
#> # ℹ n = 20
#> # ℹ 3 more variables: sample <chr>, condition <chr>, is_drug <lgl>