select: Keep or drop columns using their names and types

In stemangiola/tidySCE: Brings SingleCellExperiment to the Tidyverse

Keep or drop columns using their names and types

Description

Select (and optionally rename) variables in a data frame, using a concise mini-language that makes it easy to refer to variables based on their name (e.g. a:f selects all columns from a on the left to f on the right) or type (e.g. where(is.numeric) selects all numeric columns).

Overview of selection features

Tidyverse selections implement a dialect of R where operators make it easy to select variables:

• : for selecting a range of consecutive variables.

• ! for taking the complement of a set of variables.

• & and | for selecting the intersection or the union of two sets of variables.

• c() for combining selections.

In addition, you can use selection helpers. Some helpers select specific columns:

• everything(): Matches all variables.

• last_col(): Select last variable, possibly with an offset.

• group_cols(): Select all grouping columns.

Other helpers select variables by matching patterns in their names:

• starts_with(): Starts with a prefix.

• ends_with(): Ends with a suffix.

• contains(): Contains a literal string.

• matches(): Matches a regular expression.

• num_range(): Matches a numerical range like x01, x02, x03.

Or from variables stored in a character vector:

• all_of(): Matches variable names in a character vector. All names must be present, otherwise an out-of-bounds error is thrown.

• any_of(): Same as all_of(), except that no error is thrown for names that don't exist.

Or using a predicate function:

• where(): Applies a function to all variables and selects those for which the function returns TRUE.

Usage

## S3 method for class 'SingleCellExperiment'
select(.data, ...)

Arguments

.data	A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr). See Methods, below, for more details.
...	<tidy-select> One or more unquoted expressions separated by commas. Variable names can be used as if they were positions in the data frame, so expressions like x:y can be used to select a range of variables.

Value

An object of the same type as .data. The output has the following properties:

• Rows are not affected.

• Output columns are a subset of input columns, potentially with a different order. Columns will be renamed if new_name = old_name form is used.

• Data frame attributes are preserved.

• Groups are maintained; you can't select off grouping variables.

Methods

This function is a generic, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

The following methods are currently available in loaded packages: \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("select")}.

Examples

Here we show the usage for the basic selection operators. See the specific help pages to learn about helpers like starts_with().

The selection language can be used in functions like dplyr::select() or tidyr::pivot_longer(). Let's first attach the tidyverse:

library(tidyverse)

# For better printing
iris <- as_tibble(iris)

Select variables by name:

starwars %>% select(height)
#> # A tibble: 87 x 1
#>   height
#>    <int>
#> 1    172
#> 2    167
#> 3     96
#> 4    202
#> # i 83 more rows

iris %>% pivot_longer(Sepal.Length)
#> # A tibble: 150 x 6
#>   Sepal.Width Petal.Length Petal.Width Species name         value
#>         <dbl>        <dbl>       <dbl> <fct>   <chr>        <dbl>
#> 1         3.5          1.4         0.2 setosa  Sepal.Length   5.1
#> 2         3            1.4         0.2 setosa  Sepal.Length   4.9
#> 3         3.2          1.3         0.2 setosa  Sepal.Length   4.7
#> 4         3.1          1.5         0.2 setosa  Sepal.Length   4.6
#> # i 146 more rows

Select multiple variables by separating them with commas. Note how the order of columns is determined by the order of inputs:

starwars %>% select(homeworld, height, mass)
#> # A tibble: 87 x 3
#>   homeworld height  mass
#>   <chr>      <int> <dbl>
#> 1 Tatooine     172    77
#> 2 Tatooine     167    75
#> 3 Naboo         96    32
#> 4 Tatooine     202   136
#> # i 83 more rows

Functions like tidyr::pivot_longer() don't take variables with dots. In this case use c() to select multiple variables:

iris %>% pivot_longer(c(Sepal.Length, Petal.Length))
#> # A tibble: 300 x 5
#>   Sepal.Width Petal.Width Species name         value
#>         <dbl>       <dbl> <fct>   <chr>        <dbl>
#> 1         3.5         0.2 setosa  Sepal.Length   5.1
#> 2         3.5         0.2 setosa  Petal.Length   1.4
#> 3         3           0.2 setosa  Sepal.Length   4.9
#> 4         3           0.2 setosa  Petal.Length   1.4
#> # i 296 more rows

Operators:

The : operator selects a range of consecutive variables:

starwars %>% select(name:mass)
#> # A tibble: 87 x 3
#>   name           height  mass
#>   <chr>           <int> <dbl>
#> 1 Luke Skywalker    172    77
#> 2 C-3PO             167    75
#> 3 R2-D2              96    32
#> 4 Darth Vader       202   136
#> # i 83 more rows

The ! operator negates a selection:

starwars %>% select(!(name:mass))
#> # A tibble: 87 x 11
#>   hair_color skin_color  eye_color birth_year sex   gender    homeworld species
#>   <chr>      <chr>       <chr>          <dbl> <chr> <chr>     <chr>     <chr>  
#> 1 blond      fair        blue            19   male  masculine Tatooine  Human  
#> 2 <NA>       gold        yellow         112   none  masculine Tatooine  Droid  
#> 3 <NA>       white, blue red             33   none  masculine Naboo     Droid  
#> 4 none       white       yellow          41.9 male  masculine Tatooine  Human  
#> # i 83 more rows
#> # i 3 more variables: films <list>, vehicles <list>, starships <list>

iris %>% select(!c(Sepal.Length, Petal.Length))
#> # A tibble: 150 x 3
#>   Sepal.Width Petal.Width Species
#>         <dbl>       <dbl> <fct>  
#> 1         3.5         0.2 setosa 
#> 2         3           0.2 setosa 
#> 3         3.2         0.2 setosa 
#> 4         3.1         0.2 setosa 
#> # i 146 more rows

iris %>% select(!ends_with("Width"))
#> # A tibble: 150 x 3
#>   Sepal.Length Petal.Length Species
#>          <dbl>        <dbl> <fct>  
#> 1          5.1          1.4 setosa 
#> 2          4.9          1.4 setosa 
#> 3          4.7          1.3 setosa 
#> 4          4.6          1.5 setosa 
#> # i 146 more rows

& and | take the intersection or the union of two selections:

iris %>% select(starts_with("Petal") & ends_with("Width"))
#> # A tibble: 150 x 1
#>   Petal.Width
#>         <dbl>
#> 1         0.2
#> 2         0.2
#> 3         0.2
#> 4         0.2
#> # i 146 more rows

iris %>% select(starts_with("Petal") | ends_with("Width"))
#> # A tibble: 150 x 3
#>   Petal.Length Petal.Width Sepal.Width
#>          <dbl>       <dbl>       <dbl>
#> 1          1.4         0.2         3.5
#> 2          1.4         0.2         3  
#> 3          1.3         0.2         3.2
#> 4          1.5         0.2         3.1
#> # i 146 more rows

To take the difference between two selections, combine the & and ! operators:

iris %>% select(starts_with("Petal") & !ends_with("Width"))
#> # A tibble: 150 x 1
#>   Petal.Length
#>          <dbl>
#> 1          1.4
#> 2          1.4
#> 3          1.3
#> 4          1.5
#> # i 146 more rows

See Also

Other single table verbs: arrange(), filter(), mutate(), reframe(), rename(), slice(), summarise()

Examples

data(pbmc_small)
pbmc_small |> select(cell, orig.ident)

stemangiola/tidySCE documentation built on Sept. 22, 2024, 10:05 p.m.