Separate a character column into multiple columns with a regular expression or numeric locations

Source: R/tidyr_methods.R

[Superseded]

separate() has been superseded in favour of separate_wider_position() and separate_wider_delim() because the two functions make the two uses more obvious, the API is more polished, and the handling of problems is better. Superseded functions will not go away, but will only receive critical bug fixes.

Given either a regular expression or a vector of character positions, separate() turns a single character column into multiple columns.

# S3 method for class 'SummarizedExperiment'
separate(
  data,
  col,
  into,
  sep = "[^[:alnum:]]+",
  remove = TRUE,
  convert = FALSE,
  extra = "warn",
  fill = "warn",
  ...
)

Arguments

data

A data frame.

col

<tidy-select> Column to expand.

into

Names of new variables to create as character vector. Use NA to omit the variable in the output.

sep

Separator between columns.

If character, sep is interpreted as a regular expression. The default value is a regular expression that matches any sequence of non-alphanumeric values.

If numeric, sep is interpreted as character positions to split at. Positive values start at 1 at the far-left of the string; negative value start at -1 at the far-right of the string. The length of sep should be one less than into.

remove

If TRUE, remove input column from output data frame.

convert

If TRUE, will run type.convert() with as.is = TRUE on new columns. This is useful if the component columns are integer, numeric or logical.

NB: this will cause string "NA"s to be converted to NAs.

extra

If sep is a character vector, this controls what happens when there are too many pieces. There are three valid options:

  • "warn" (the default): emit a warning and drop extra values.

  • "drop": drop any extra values without a warning.

  • "merge": only splits at most length(into) times

fill

If sep is a character vector, this controls what happens when there are not enough pieces. There are three valid options:

  • "warn" (the default): emit a warning and fill from the right

  • "right": fill with missing values on the right

  • "left": fill with missing values on the left

...

Additional arguments passed on to methods.

Value

tidySummarizedExperiment

References

Hutchison, W.J., Keyes, T.J., The tidyomics Consortium. et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 21, 1166–1170 (2024). https://doi.org/10.1038/s41592-024-02299-2

Wickham, H., Vaughan, D. (2023). tidyr: Tidy Messy Data. R package version 2.0.0, https://CRAN.R-project.org/package=tidyr

See also

unite(), the complement, extract() which uses regular expression capturing groups.

Examples

un <- tidySummarizedExperiment::pasilla |>
    unite("group", c(condition, type))
#> tidySummarizedExperiment says: Key columns are missing. A data frame is returned for independent data analysis.
un |> separate(col=group, into=c("condition", "type"))
#> Warning: Expected 2 pieces. Additional pieces discarded in 7 rows [1, 2, 3, 4, 5, 6, 7].
#> class: SummarizedExperiment 
#> dim: 14599 7 
#> metadata(0):
#> assays(1): counts
#> rownames(14599): FBgn0000003 FBgn0000008 ... FBgn0261574 FBgn0261575
#> rowData names(0):
#> colnames(7): untrt1 untrt2 ... trt2 trt3
#> colData names(2): condition type