launch_msfinder_annotation: Annotates peaks based on files extracted from MSFinder.

In eMetaboHUB/MS-CleanR: Cleans MS Data for Easier Analyses

Annotates peaks based on files extracted from MSFinder.

Description

Annotates peaks based on files extracted from MSFinder.

Usage

launch_msfinder_annotation(
  compound_levels = NULL,
  biosoc_levels = c("generic"),
  levels_scores = NULL,
  score_only = FALSE,
  other_peaks_warning = FALSE
)

Arguments

compound_levels	A vector containing the compound levels to consider, in the given order.
biosoc_levels	A vector containing the biosource levels to consider, in the given order.
levels_scores	A list of levels names and their corresponding multiplier to adapt final annotation scores.
score_only	Whether to find the most probable annotation on scores only (without using the biosoc_levels and compound_levels)
other_peaks_warning	Whether to issue a warning if other possible annotated peaks exists in the cluster

Architecture needed by launch_msfinder_annotation in the project_directory

• pos

  • msf_X

    Formula<...>.txt

    Formulas for possible identifications in the X biosoc level, exported from MSFinder

    Structure<...>.txt

    Structures for possible identifications in the X biosoc level, exported from MSFinder

• neg

  • msf_X

    Formula<...>.txt

    Formulas for possible identifications in the X biosoc level, exported from MSFinder

    Structure<...>.txt

    Structures for possible identifications in the X biosoc level, exported from MSFinder

• intermediary_data

  samples.csv

  Information on samples

  final_peaks_data.csv

  Peaks remaining after all filters have been applied

  links_ms-final.csv

  Links between peaks indicated by MSDial (global) and adducts/neutral losses detection (by cluster)

Output files of launch_msfinder_annotation in the project directory

annotated_data-cleaned.csv

Final auto-annotated data with only relevant peaks

• intermediary_data

  identifying_data.csv

  Union of MSDial and MSFinder data, with clusters info

  annotated_data.csv

  Final auto-annotated data, complete with all possibilities

  annotated_data-manual_check.csv

  Final auto-annotated data for clusters needing manual checking (only created in this case)

eMetaboHUB/MS-CleanR documentation built on Jan. 3, 2024, 8:55 p.m.