Filter cell meta data in ReadPNA_Seurat

[ludvigla]

Description

This PR adds a meta data filter to ReadPNA_Seurat to keep the meta.data slot clean. Full meta data can be obtained by setting detailed_meta_data = TRUE.

The columns to keep are defined in the CELL_META_COLS variable. Currently, these are:

CELL_META_COLS <- c(
  "n_umi", "n_edges", "n_antibodies", "isotype_fraction",
  "average_k_core", "reads_in_component", "tau", "tau_type",
  "n_umi1", "n_umi2", "sample"
)

Fixes: PNA-3078

Type of change

• Bug fix (non-breaking change which fixes an issue).
• New feature (non-breaking change which adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

How Has This Been Tested?

Added new test to tests/testthat/test-ReadPNA_Seurat.R

PR checklist:

• My changes generate no new warnings.
• I have added tests that prove my fix is effective or that my feature works.
• I have documented any significant changes to the code in CHANGELOG.md

[Copilot]

Pull request overview

Adds an opt-in mechanism to retain full per-cell metadata when loading PNA PXL files into Seurat, while defaulting to a curated subset of QC-relevant columns to keep meta.data smaller/cleaner (Fixes: PNA-2926).

Changes:

• Added detailed_meta_data argument to ReadPNA_Seurat(); when FALSE it filters meta.data to CELL_META_COLS.
• Introduced CELL_META_COLS as a central definition of which cell metadata columns are retained by default.
• Updated documentation, changelog, and added a test to cover the new behavior.

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
R/load_data_pna.R	Adds detailed_meta_data parameter, validates it, and filters cell metadata by default.
R/aaa.R	Defines CELL_META_COLS constant used for default metadata filtering.
tests/testthat/test-ReadPNA_Seurat.R	Adds a test asserting detailed metadata loads more columns than the default.
man/ReadPNA_Seurat.Rd	Documents the new detailed_meta_data argument.
CHANGELOG.md	Notes the new default metadata filtering behavior and how to opt into detailed metadata.

Files not reviewed (1)

• man/ReadPNA_Seurat.Rd: Generated file

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[maxkarlsson]

I think we should drop tau!

[maxkarlsson]

Looks good!