Select one or more values from each context. By default omitting an expression for a context is the same as selecting NOTHING from that context.
The <tidy-select> implementation within
biocmask is almost similar to dplyr except when used within the
across() function. When used from accross(), the data provided to
eval_select is a zero length slice of the data.
This was an intentional choice to prevent the evaluation of potentionally
expensive chopping operations for S4Vectors. This means that predicate
function from where() will NOT be able to query the
original data.
Usage
# S3 method for class 'SummarizedExperiment'
select(.data, ...)Arguments
- .data
a
SummarizedExperimentobject- ...
<
tidy-select> one or more selection expressions. Supports wrapping expressions within the <biocmask-contexts>.
Examples
# only keep assays, other contexts are dropped
select(se_simple, everything())
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | counts logcounts | |
#> <chr> <chr> | <int> <dbl> | |
#> 1 row_1 col_1 | 14 2.64 | |
#> 2 row_2 col_1 | 19 2.94 | |
#> 3 row_3 col_1 | 16 2.77 | |
#> 4 row_4 col_1 | 11 2.40 | |
#> 5 row_5 col_1 | 18 2.89 | |
#> … … … … …
#> n-4 row_1 col_4 | 9 2.20 | |
#> n-3 row_2 col_4 | 4 1.39 | |
#> n-2 row_3 col_4 | 20 3.00 | |
#> n-1 row_4 col_4 | 3 1.10 | |
#> n row_5 col_4 | 5 1.61 | |
#> # ℹ n = 20
# only keep rowData, other contexts are dropped
select(se_simple, rows(everything()))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | | gene length direction |
#> <chr> <chr> | | <chr> <int> <chr> |
#> 1 row_1 col_1 | | g1 1 - |
#> 2 row_2 col_1 | | g2 24 + |
#> 3 row_3 col_1 | | g3 60 + |
#> 4 row_4 col_1 | | g4 39 - |
#> 5 row_5 col_1 | | g5 37 + |
#> … … … … … …
#> n-4 row_1 col_4 | | g1 1 - |
#> n-3 row_2 col_4 | | g2 24 + |
#> n-2 row_3 col_4 | | g3 60 + |
#> n-1 row_4 col_4 | | g4 39 - |
#> n row_5 col_4 | | g5 37 + |
#> # ℹ n = 20
select(se_simple, rows(where(is.numeric)))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | | length |
#> <chr> <chr> | | <int> |
#> 1 row_1 col_1 | | 1 |
#> 2 row_2 col_1 | | 24 |
#> 3 row_3 col_1 | | 60 |
#> 4 row_4 col_1 | | 39 |
#> 5 row_5 col_1 | | 37 |
#> … … … …
#> n-4 row_1 col_4 | | 1 |
#> n-3 row_2 col_4 | | 24 |
#> n-2 row_3 col_4 | | 60 |
#> n-1 row_4 col_4 | | 39 |
#> n row_5 col_4 | | 37 |
#> # ℹ n = 20
# Note on `where()` clause, all data is available within select
select(se_simple, rows(where(~any(grepl("-", .x)))))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | | direction |
#> <chr> <chr> | | <chr> |
#> 1 row_1 col_1 | | - |
#> 2 row_2 col_1 | | + |
#> 3 row_3 col_1 | | + |
#> 4 row_4 col_1 | | - |
#> 5 row_5 col_1 | | + |
#> … … … …
#> n-4 row_1 col_4 | | - |
#> n-3 row_2 col_4 | | + |
#> n-2 row_3 col_4 | | + |
#> n-1 row_4 col_4 | | - |
#> n row_5 col_4 | | + |
#> # ℹ n = 20
# within an `across()`, only a zero-length slice avialble, so the
# `where()` predicate cannot access the data
mutate(se_simple,
rows(
across(where(~any(grepl("-", .x))),
~sprintf("%s foo", .x))))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | counts logcounts | gene length direction | sample
#> <chr> <chr> | <int> <dbl> | <chr> <int> <chr> | <chr>
#> 1 row_1 col_1 | 14 2.64 | g1 1 - | s1
#> 2 row_2 col_1 | 19 2.94 | g2 24 + | s1
#> 3 row_3 col_1 | 16 2.77 | g3 60 + | s1
#> 4 row_4 col_1 | 11 2.40 | g4 39 - | s1
#> 5 row_5 col_1 | 18 2.89 | g5 37 + | s1
#> … … … … … … … … …
#> n-4 row_1 col_4 | 9 2.20 | g1 1 - | s4
#> n-3 row_2 col_4 | 4 1.39 | g2 24 + | s4
#> n-2 row_3 col_4 | 20 3.00 | g3 60 + | s4
#> n-1 row_4 col_4 | 3 1.10 | g4 39 - | s4
#> n row_5 col_4 | 5 1.61 | g5 37 + | s4
#> # ℹ n = 20
#> # ℹ 1 more variable: condition <chr>
# here is an acceptable usage of the `where()` predicate
mutate(se_simple,
rows(
across(where(is.character),
~sprintf("%s foo", .x))))
#> # A SummarizedExperiment-tibble Abstraction: 5 × 4
#> .features .samples | counts logcounts | gene length direction | sample
#> <chr> <chr> | <int> <dbl> | <chr> <int> <chr> | <chr>
#> 1 row_1 foo col_1 | 14 2.64 | g1 foo 1 - foo | s1
#> 2 row_2 foo col_1 | 19 2.94 | g2 foo 24 + foo | s1
#> 3 row_3 foo col_1 | 16 2.77 | g3 foo 60 + foo | s1
#> 4 row_4 foo col_1 | 11 2.40 | g4 foo 39 - foo | s1
#> 5 row_5 foo col_1 | 18 2.89 | g5 foo 37 + foo | s1
#> … … … … … … … … … … … …
#> n-4 row_1 foo col_4 | 9 2.20 | g1 foo 1 - foo | s4
#> n-3 row_2 foo col_4 | 4 1.39 | g2 foo 24 + foo | s4
#> n-2 row_3 foo col_4 | 20 3.00 | g3 foo 60 + foo | s4
#> n-1 row_4 foo col_4 | 3 1.10 | g4 foo 39 - foo | s4
#> n row_5 foo col_4 | 5 1.61 | g5 foo 37 + foo | s4
#> # ℹ n = 20
#> # ℹ 1 more variable: condition <chr>