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Declare a column contract for vendor exports

Source: R/import.R
cr_column_map.Rd

Segmented single-cell exports name their columns however the acquisition software happens to. A cr_column_map records how those raw headers translate to the analysis names used downstream, so that the mapping lives in one declarative object instead of being spread through reader code.

Usage

cr_column_map(exact = NULL, prefix = NULL, keep = NULL)

# S3 method for class 'cr_column_map'
print(x, ...)

Arguments

exact

Named character vector. Names are raw header names, values the analysis name to rename them to.

prefix

Named character vector. Names are regular expressions matched against the raw header names, values the analysis name. The first matching column is renamed.

keep

Optional character vector of analysis names to retain after renaming, in this order. Names that are absent are ignored. NULL keeps every column.

x

A cr_column_map.

...

Ignored.

Value

An object of class cr_column_map: a list with elements exact, prefix and keep.

x, invisibly.

Details

Two matching modes are available because vendor headers are not always stable: exact matches a header verbatim, while prefix matches a regular expression. Prefix matching exists for headers that embed a unit glyph (an area column ending in a squared-micrometre symbol, for instance), where the exact spelling cannot be relied on.

Renaming is deliberately tolerant: names that do not occur in a given export are skipped silently rather than raising an error. Exports from the same instrument routinely carry different subsets of the available measurements, and a strict renamer forces a second reader to exist for every subset.

See also

cr_read_export(), cr_read_exports().

Other import: cr_assign_units(), cr_centroid_overlap(), cr_extract_markers(), cr_filename_grammar(), cr_marker_rules(), cr_merge_rules(), cr_parse_paths(), cr_path_spec(), cr_read_cellprofiler(), cr_read_cells(), cr_read_design(), cr_read_export(), cr_read_exports(), cr_read_qupath(), cr_read_segmantr(), cr_unit_map()

Examples

map <- cr_column_map(
  exact = c(
    "Event Label" = "cell_id",
    "Signal - Mean Intensity" = "target_signal"
  ),
  prefix = c("^Nuclei - Area" = "area"),
  keep = c("cell_id", "target_signal", "area")
)
map
#> <cr_column_map>
#> • exact rules: 2
#> • prefix rules: 1
#> • keep: 3 columns