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Filter an MGF file to keep only spectra for features present in mmo$feature_data$id

filter_mgf_to_mmo.Rd

Create a new .mgf file that contains only spectra (ION blocks) whose FEATURE_ID occurs in mmo$feature_data$id. This is useful for keeping your spectral library in sync with the features currently stored in an mmo object (e.g., after subsetting, filtering, or rebuilding an mmo).

Usage

filter_mgf_to_mmo(
  mmo,
  mgf_path,
  output_path = NULL,
  chunk_lines = 100000L,
  verbose = TRUE
)

Arguments

mmo

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

mgf_path

Character. Path to the input .mgf file.

output_path

Character or NULL. Path to write the filtered .mgf. If NULL (default), the output name is derived from mgf_path by appending _filtered before the .mgf extension (or adding _filtered.mgf if no extension is present).

chunk_lines

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

verbose

Logical. If TRUE (default), prints a short progress summary and final counts.

Value

Invisibly returns a list with:

  • output_path: path to the filtered MGF

  • blocks_total: total BEGIN IONS blocks encountered

  • blocks_kept: number of blocks written to output_path

  • lines_read: total lines read from mgf_path

Details

Each spectrum in an MGF is represented by a BEGIN IONS ... END IONS block. This function keeps or discards entire blocks based on the integer value in the FEATURE_ID= header line. All blocks (MS1 and MS2) are kept for a retained feature, including multiple MS2 blocks if present.

Examples

if (FALSE) { # \dontrun{
# Write "<input>_filtered.mgf" containing only FEATURE_IDs present in mmo$feature_data$id
filter_mgf_to_mmo(mmo, "spectra.mgf")

# Write to a custom file name
filter_mgf_to_mmo(mmo, "spectra.mgf", output_path = "spectra_mmo_only.mgf")
} # }