R/tidyr_methods.R
extract.Rd
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has been superseded in favour of separate_wider_regex()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Superseded functions will not go away, but will only receive critical bug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 'SummarizedExperiment'
extract(
data,
col,
into,
regex = "([[:alnum:]]+)",
remove = TRUE,
convert = FALSE,
...
)
A data frame.
<tidy-select
> Column to expand.
Names of new variables to create as character vector.
Use NA
to omit the variable in the output.
A string representing a regular expression used to extract the
desired values. There should be one group (defined by ()
) for each
element of into
.
If TRUE
, remove input column from output data frame.
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 NA
s.
Additional arguments passed on to methods.
tidySummarizedExperiment
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
separate()
to split up by a separator.
tidySummarizedExperiment::pasilla |>
extract(type, into="sequencing", regex="([a-z]*)_end", convert=TRUE)
#> 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 sequencing