Load and Validate a Manifest for Immune Repertoire Files

Source code

Description

This function loads a manifest from either a file path or a data frame, validates the presence of a column with repertoire file paths, and converts all file paths to absolute paths. It is used to support flexible pipelines for loading bulk or single-cell immune repertoire data across samples.

If the input is a file path, the function reads it with readr::read_delim. If the input is a data frame, it checks whether file paths are absolute; relative paths are only allowed when the manifest is loaded from a file.

It warns the user if many of the files listed in the manifest are missing, and stops execution if none of the files exist.

The column with file paths is normalized into the internal filename schema.

Usage

read_manifest(
  manifest,
  file_col = "file",
  delim = NULL,
  ...,
  verbose = getOption("immundata.verbose", TRUE)
)

Arguments

manifest	A manifest table. Can be either: a data frame with per-file annotations, or a path to a CSV/TSV/TXT manifest file.
file_col	A string specifying the name of the column in the manifest that contains paths to repertoire files. Defaults to “file”.
delim	Delimiter used to read the manifest file. If NULL, it is inferred from the extension: comma for .csv, tab for .tsv and .txt.
…	Additional arguments passed to readr::read_delim() when reading a manifest from a file.
verbose	Logical(1). Whether to print informative messages. Defaults to getOption(“immundata.verbose”, TRUE).

Value

A validated and updated manifest data frame with absolute file paths and an additional internal column named imd_filename.