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Annotate mmo$feature_info with MS2 presence and MS2 block counts from an MGF

annotate_feature_info_ms2_from_mgf.Rd

Scan an .mgf file and summarize MS/MS availability for each feature in mmo$feature_info. The function adds two columns:

  • ms2: TRUE if the MGF contains at least one MSLEVEL=2 block for that id; otherwise FALSE.

  • count_ms2: number of MSLEVEL=2 blocks for that id.

Usage

annotate_feature_info_ms2_from_mgf(
  mmo,
  mgf_path,
  chunk_lines = 100000L,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

mmo

An ecomet mmo object containing a required feature_info table with an id column (mmo$feature_info$id).

mgf_path

Character. Path to the input .mgf file.

chunk_lines

Integer. Number of lines read per iteration. Larger values are typically faster but use more memory. Default is 100000L.

overwrite

Logical. If FALSE (default) and ms2 and/or count_ms2 already exist in mmo$feature_info, the function errors. Set overwrite = TRUE to replace existing columns.

verbose

Logical. If TRUE (default), prints a brief summary of how many MS2 blocks were found and how many features have MS2.

Value

The updated mmo object with mmo$feature_info$ms2 and mmo$feature_info$count_ms2 added (or overwritten if overwrite = TRUE).

Details

This is useful for quickly identifying which features have MS/MS spectra available (and how many replicate MS2 spectra exist) before downstream annotation, networking, or library-building steps.

Examples

if (FALSE) { # \dontrun{
# Add ms2 + count_ms2 columns to mmo$feature_info
mmo <- annotate_feature_info_ms2_from_mgf(mmo,
       "spectra.mgf")

# Overwrite existing columns if you re-run on a different MGF
mmo <- annotate_feature_info_ms2_from_mgf(mmo,
       "spectra_new.mgf", overwrite = TRUE)
} # }