as_tibble: Coerce lists, matrices, and more to data frames

In stemangiola/tidySE: Brings SummarizedExperiment to the Tidyverse

Coerce lists, matrices, and more to data frames

Description

as_tibble() turns an existing object, such as a data frame or matrix, into a so-called tibble, a data frame with class tbl_df. This is in contrast with tibble(), which builds a tibble from individual columns. as_tibble() is to tibble() as base::as.data.frame() is to base::data.frame().

as_tibble() is an S3 generic, with methods for:

• data.frame: Thin wrapper around the list method that implements tibble's treatment of rownames.

• matrix, poly, ts, table

• Default: Other inputs are first coerced with base::as.data.frame().

as_tibble_row() converts a vector to a tibble with one row. If the input is a list, all elements must have size one.

as_tibble_col() converts a vector to a tibble with one column.

Usage

## S3 method for class 'SummarizedExperiment'
as_tibble(
  x,
  ...,
  .name_repair = c("check_unique", "unique", "universal", "minimal"),
  rownames = pkgconfig::get_config("tibble::rownames", NULL)
)

Arguments

x	A data frame, list, matrix, or other object that could reasonably be coerced to a tibble.
...	Unused, for extensibility.
.name_repair	Treatment of problematic column names: "minimal": No name repair or checks, beyond basic existence, "unique": Make sure names are unique and not empty, "check_unique": (default value), no name repair, but check they are unique, "universal": Make the names unique and syntactic a function: apply custom name repair (e.g., .name_repair = make.names for names in the style of base R). A purrr-style anonymous function, see rlang::as_function() This argument is passed on as repair to vctrs::vec_as_names(). See there for more details on these terms and the strategies used to enforce them.
rownames	How to treat existing row names of a data frame or matrix: NULL: remove row names. This is the default. NA: keep row names. A string: the name of a new column. Existing rownames are transferred into this column and the row.names attribute is deleted. No name repair is applied to the new column name, even if x already contains a column of that name. Use as_tibble(rownames_to_column(...)) to safeguard against this case. Read more in rownames.

Value

tibble

Row names

The default behavior is to silently remove row names.

New code should explicitly convert row names to a new column using the rownames argument.

For existing code that relies on the retention of row names, call pkgconfig::set_config("tibble::rownames" = NA) in your script or in your package's .onLoad() function.

Life cycle

Using as_tibble() for vectors is superseded as of version 3.0.0, prefer the more expressive as_tibble_row() and as_tibble_col() variants for new code.

See Also

tibble() constructs a tibble from individual columns. enframe() converts a named vector to a tibble with a column of names and column of values. Name repair is implemented using vctrs::vec_as_names().

Examples

tidySummarizedExperiment::pasilla %>%
    as_tibble()
    
tidySummarizedExperiment::pasilla %>%
    as_tibble(.subset=-c(condition, type))

stemangiola/tidySE documentation built on June 2, 2024, 9:51 a.m.