biocmask contexts — biocmask-context • biocmask

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

Usage

cols(...)

rows(...)

col_ctx(x, asis = FALSE)

row_ctx(x, asis = FALSE)

assay_ctx(x, asis = FALSE)

Arguments

x, ...: expressions to evaluate within its associated context
asis: asis = FALSE (the default) will indicate using active bindings that attempt to coerce the underlying data into a format that is appropriate for the current context. Indicating TRUE will instead bind the underlying data as is.

Value

function called for its side-effects

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>