Extract a character column into multiple columns using regular expression groups

Source: R/tidyr_methods.R

[Superseded]

extract() has been superseded in favour of separate_wider_regex() because it has a more polished API and better handling of problems. Superseded functions will not go away, but will only receive critical bug fixes.

Given a regular expression with capturing groups, extract() turns each group into a new column. If the groups don't match, or the input is NA, the output will be NA.

# S3 method for class 'SingleCellExperiment'
extract(
  data,
  col,
  into,
  regex = "([[:alnum:]]+)",
  remove = TRUE,
  convert = FALSE,
  ...
)

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.

regex

A string representing a regular expression used to extract the desired values. There should be one group (defined by ()) for each element of 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.

...

Additional arguments passed on to methods.

Value

`tidySingleCellExperiment`

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, Averick M, Bryan J, Chang W, McGowan LD, François R, et al. Welcome to the tidyverse. Journal of Open Source Software. 2019;4(43):1686. https://doi.org/10.21105/joss.01686

See also

separate() to split up by a separator.

Examples

data(pbmc_small)
pbmc_small |>
  extract(groups,
    into="g",
    regex="g([0-9])",
    convert=TRUE)
#> # A SingleCellExperiment-tibble abstraction: 80 × 17
#> # Features=230 | Cells=80 | Assays=counts, logcounts
#>    .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents     g
#>    <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <int>
#>  1 ATGCC… SeuratPro…         70           47 0               A                 2
#>  2 CATGG… SeuratPro…         85           52 0               A                 1
#>  3 GAACC… SeuratPro…         87           50 1               B                 2
#>  4 TGACT… SeuratPro…        127           56 0               A                 2
#>  5 AGTCA… SeuratPro…        173           53 0               A                 2
#>  6 TCTGA… SeuratPro…         70           48 0               A                 1
#>  7 TGGTA… SeuratPro…         64           36 0               A                 1
#>  8 GCAGC… SeuratPro…         72           45 0               A                 1
#>  9 GATAT… SeuratPro…         52           36 0               A                 1
#> 10 AATGT… SeuratPro…        100           41 0               A                 1
#> # ℹ 70 more rows
#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
#> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
#> #   tSNE_2 <dbl>