change_params_small: Change Params Small

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Change Params Small

Description

This function helps changing convenience parameters.

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,
  summarise = NULL
)

Arguments

fil_pat	The pattern identifying your whole job. You can put whatever you want. STRING
fil_fea_raw	The path to the file containing your features' intensities. Can be generated by mzmine3 or SLAW. STRING
fil_met_raw	The path to the file containing your metadata. If your experiment contains a single taxon, you can provide it below instead. STRING
fil_sir_raw	The directory containing the sirius annotations. STRING
fil_spe_raw	The path to the file containing your features' spectra. Can contain MS1 and/or MS2 spectra. STRING
ms_pol	The polarity used. Must be either "pos" or "neg". STRING
org_tax	If your experiment contains a single taxon, its scientific name. "Homo sapiens". STRING
hig_con	Filter high confidence candidates only. BOOLEAN
summarise	Summarize all candidates per feature to a single row. BOOLEAN

Value

YAML file with changed parameters.

Examples

## Not run: 
tima:::copy_backbone()
tima::change_params_small(
  fil_pat = "myExamplePattern",
  fil_fea_raw = "myExampleDir/myExampleFeatures.csv",
  fil_met_raw = "myExampleDir2SomeWhereElse/myOptionalMetadata.tsv",
  fil_sir_raw = "myExampleDir3/myAwesomeSiriusProject.zip",
  fil_spe_raw = "myBeautifulSpectra.mgf",
  ms_pol = "pos",
  org_tax = "Gentiana lutea",
  hig_con = TRUE,
  summarise = FALSE
)

## End(Not run)

taxonomicallyinformedannotation/tima-r documentation built on Nov. 24, 2024, 9:34 p.m.