change_params_small

Change Parameters (Convenience Function)

Description

Updates TIMA workflow parameters for quick setup with a simplified interface. This function modifies the prepare_params YAML configuration file by copying provided input files to the appropriate directories and updating parameter values. Implements SOLID principles with clear separation of concerns.

Usage

change_params_small(
  fil_pat = NULL,
  fil_fea_raw = NULL,
  fil_met_raw = NULL,
  fil_sir_raw = NULL,
  fil_spe_raw = NULL,
  ms_pol = NULL,
  org_tax = NULL,
  hig_con = NULL,
  summarize = NULL,
  cache_dir = NULL
)

Arguments

fil_pat Character. Job identifier/pattern for output files (optional)

fil_fea_raw Character. Path to features file (e.g., from MZmine/SIRIUS)

fil_met_raw Character. Path to metadata file (optional if single taxon)

fil_sir_raw Character. Path to SIRIUS annotations directory/zip

fil_spe_raw Character. Path to spectra file (MGF format with MS1/MS2)

ms_pol Character. MS polarity: "pos" or "neg"

org_tax Character. Scientific name for single-taxon experiments

hig_con Logical. Filter for high confidence candidates only

summarize Logical. Summarize all candidates per feature to single row

cache_dir Character. Cache directory path (for testing; uses go_to_cache() if NULL)

Details

This function:

Validates all input files exist before copying
Copies files to standardized cache locations
Updates the prepare_params YAML configuration
Handles NA values properly for YAML null representation

Value

Invisible NULL. Modifies prepare_params YAML as side effect.

Examples

library("tima")

# Setup complete workflow parameters
copy_backbone()
change_params_small(
  fil_pat = "gentiana_experiment",
  fil_fea_raw = "data/raw/features.csv",
  fil_met_raw = "data/raw/metadata.tsv",
  fil_sir_raw = "data/raw/sirius_output.zip",
  fil_spe_raw = "data/raw/spectra.mgf",
  ms_pol = "pos",
  org_tax = "Gentiana lutea",
  hig_con = TRUE,
  summarize = FALSE
)