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Preprocess Spectronaut reports

Source: R/Preprocessing.R
preprocess_spectronaut.Rd

Converts a Spectronaut report (long TSV format) into three structured tables: run metadata, protein identification and protein quantification.

The report has to carry the right columns, and rather than leave that to be reconstructed by hand the package ships the Spectronaut export schema that produces them:

system.file("extdata", "NADIA_Report.rs", package = "NADIA")

Import that file into Spectronaut as a report schema and export with it. The result has the shape of nadia_dia_report.tsv.gz, the example that ships alongside it.

Usage

preprocess_spectronaut(
  file_path,
  condition_order,
  export_dir = NULL,
  agg_coverage_run = c("max", "mean", "median", "min"),
  agg_coverage_global = c("max", "mean", "median", "min"),
  agg_mw = c("max", "mean", "median", "min"),
  agg_cscore_runwise = c("mean", "max", "median", "min"),
  timestamp_suffix = TRUE,
  verbose = TRUE
)

Arguments

file_path

Path to the Spectronaut TSV file.

condition_order

Character vector that selects the experimental conditions to retain and sets their order in subsequent analysis stages (e.g. c("Control", "Treated")). Runs whose condition is not listed are dropped; conditions listed but absent from the report are dropped too, with a warning, so that no empty factor level reaches the metadata.

export_dir

Directory to export the TSV files to. If NULL (default), no files are exported.

agg_coverage_run

Aggregation method for the per-sample PG.Coverage. Options: "max" (default), "mean", "median", "min".

agg_coverage_global

Aggregation method for PG.Coverage.Global. Options: "max" (default), "mean", "median", "min".

agg_mw

Aggregation method for PG.MolecularWeight. Options: "max" (default), "mean", "median", "min".

agg_cscore_runwise

Aggregation method for PG.Cscore.RunWise. Options: "mean" (default), "max", "median", "min".

timestamp_suffix

Logical. If TRUE (default), appends a timestamp to the names of the exported files.

verbose

Logical. If TRUE (default), shows progress messages.

Value

A list with class spectronaut_data containing:

metadata

Data frame with the run information (1 row per sample)

protein_id

Data frame with the identification metrics per protein

protein_quant

Data frame with the quantification metrics per protein

The call that produced the object and a fingerprint of the file it was read from (path, size, modification time and MD5) travel with it as the attributes nadia_call and nadia_source. They are attributes rather than list elements so that the three-element structure above is unchanged; write_nadia() records them as the provenance of an analysis.

Examples

# A trimmed Spectronaut report ships with the package
report <- system.file("extdata", "nadia_dia_report.tsv.gz", package = "NADIA")

prep <- preprocess_spectronaut(report,
                               condition_order = c("A", "B", "D"),
                               verbose = FALSE)
prep
#> Preprocessed Spectronaut data
#> -----------------------------
#> Runs (metadata): 12 
#> Proteins (ID): 2000 
#> Proteins (QUANT): 2000 
#> 
#> Conditions: A, B, D 
dim(prep$protein_quant)
#> [1] 2000   44

# Nothing is written to disk unless export_dir is given
prep <- preprocess_spectronaut(report,
                               condition_order = c("A", "B", "D"),
                               export_dir = tempdir(),
                               verbose = FALSE)