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Declare how files are merged into analysis units

Source: R/import-units.R
cr_merge_rules.Rd

States which replicate suffixes and marker flags mean "these files are one unit" and which mean "these files are different units". Getting this wrong is silent in both directions, so each rule is explicit.

Usage

cr_merge_rules(
  merge_suffix = "\\.1$",
  merge_marker = "merge_unit",
  keep_separate = "\\.2$",
  reacquisition = "reacquisition",
  merge_reacquisition = TRUE,
  separate_suffix = "re"
)

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

Arguments

merge_suffix

Regular expression matched against the replicate index, marking a second acquisition pass. NULL disables.

merge_marker

Name of a logical column that must be TRUE for a merge_suffix match to merge, or NULL to merge on the suffix alone. When the column is absent no suffix merging happens.

keep_separate

Regular expression matched against the replicate index, marking indices that must never merge. NULL disables.

reacquisition

Name of a logical column marking repeated reads, or NULL.

merge_reacquisition

Logical. Fold repeated reads into their plain sibling. Default TRUE.

separate_suffix

Suffix appended to the replicate index of a repeated read when merge_reacquisition = FALSE. Default "re".

x

A cr_merge_rules.

...

Ignored.

Value

An object of class cr_merge_rules (a list).

x, invisibly.

Details

  • merge_suffix matches the replicate index of a file that is the second pass over a unit that already exists. Left unmerged, such a unit draws a full cell allocation twice and is double-weighted in its own batch.

  • merge_marker names a logical column (typically produced by cr_extract_markers()) that must also be TRUE before a suffix match is merged. Requiring the marker is the conservative default: a suffix on its own is not evidence.

  • keep_separate matches replicate indices that look mergeable but are a different physical unit. It always wins over merge_suffix. cr_centroid_overlap() is the evidence test for deciding which of the two a given suffix is.

  • reacquisition names the logical column marking a repeated read. With merge_reacquisition = TRUE such a file folds into its plain sibling; otherwise separate_suffix is appended so it stays a unit of its own.

See also

cr_assign_units(), cr_extract_markers(), cr_centroid_overlap().

Other import: cr_assign_units(), cr_centroid_overlap(), cr_column_map(), cr_extract_markers(), cr_filename_grammar(), cr_marker_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

cr_merge_rules()
#> <cr_merge_rules>
#> • merge suffix: "\\.1$"
#> • gated on marker: "merge_unit"
#> • kept separate: "\\.2$"
#> • merge repeated reads: TRUE
cr_merge_rules(merge_marker = NULL, keep_separate = NULL)
#> <cr_merge_rules>
#> • merge suffix: "\\.1$"
#> • gated on marker: "no"
#> • kept separate: "disabled"
#> • merge repeated reads: TRUE