Import Skyline peak integration results — import_data

This function imports tabular data files (*.csv) exported from Skyline, containing peak integration results.

Usage

import_data_skyline(
  data = NULL,
  path,
  transition_id_columns = c("name", "mz", "none"),
  import_metadata = TRUE,
  silent = FALSE
)

Arguments

data: A MRMhubExperiment object.
path: One or more file paths, or a directory path from which all matching files will be imported.
transition_id_columns: A character vector specifying the columns that define the transition (precursor and product) to use for unique feature_id generation. Options are "name", "mz", or "none". If "none", feature_id is derived from Molecule Name and Precursor Name or Product Name. If "mz", feature_id is based on Precursor Mz and Product Mz. Using "none" will result in feature_id being a copy of Molecule Name, with an error raised if it is not unique for each transition.
import_metadata: Logical; whether to import additional metadata columns (e.g., precursor/product m/z values).
silent: Logical; whether to suppress most notifications.

Value

A MRMhubExperiment object containing the imported data.

Details

In Skyline, transitions are defined by the Molecule Name and corresponding precursor and product m/z values, rather than any identifier. When importing this data, the feature_id is generated using the Molecule Name with either precursor/product names or m/z values, unless Molecule Name uniquely identifies the features (refer to the transition_id_columns argument below).

The following supported columns from Skyline can be imported:

Skyline Column Name	MRMhub Column Name	Required
`Replicate Name`	`analysis_id`	Yes
`Molecule List Name`	`feature_class`	No
`Molecule Name`	`feature_id`	Yes
`Precursor Name`	`feature_id`	Yes*
`Product Name`	`feature_id`	Yes*
`Precursor Mz`	`method_precursor_mz`	Yes*
`Product Mz`	`method_product_mz`	Yes*
`Area`	`feature_area`	Yes
`Retention Time`	`feature_rt`	No

*Requirements for these columns are described in transition_id_columns.

To export results from Skyline, use the 'Molecule Transition Results' format and include Replicate Name, Molecule Name, and either Precursor Mz/Product Mz or Precursor Name/Product Name columns. At least one feature variable, such as Area or RT, must also be exported.

Identifier normalization

All imported identifiers are whitespace-normalized on import: leading and trailing spaces are removed and internal runs of whitespace are collapsed to a single space (for example "QC 01" becomes "QC 01"). Raw-data file extensions (.mzML, .d, .raw, .wiff, .wiff2, .lcd, .chrom, case-insensitive) are stripped from analysis_id.

The same normalization is applied to both the data and the metadata, which is what lets an analysis_id typed into metadata match the one derived from a data-file name instead of silently failing to join. A consequence is that two identifiers differing only by whitespace collapse to one and are then reported as duplicates.

Examples

mexp <- MRMhubExperiment()
file_path <- system.file("extdata", "Skyline_MoleculeTransitionResults.csv", package = "mrmhub")
mexp <- import_data_skyline(
  data = mexp,
  path = file_path,
  transition_id_columns = "mz",
  import_metadata = TRUE
)
#> ✔ Imported 6 analyses with 21 features.
#> ℹ feature_area selected as default feature intensity. Modify with `set_intensity_var()`.
#> ✔ Analysis metadata associated with 6 analyses.
#> ✔ Feature metadata associated with 21 features.
#> ℹ Analysis order was based on `analysis_order` column of imported data. Use `set_analysis_order` to change the order.
print(mexp)
#> 
#> ── MRMhubExperiment:  ──────────────────────────────────────────────────────────
#> NA | 6 analyses and 21 features | signal: feature_area
#> Last step: Annotated raw AREA values
#> Normalized ✖ Quantitated ✖ Drift/batch ✖ Filtered ✖
#> ℹ Use `mrmhub_status()` for the full processing and metadata report