library("tima")
copy_backbone()
::change_params_small(
timafil_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,
summarize = FALSE
)
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,
summarize = 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 mzmine, SLAW, or SIRIUS. 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 |
summarize
|
Summarize all candidates per feature to a single row. BOOLEAN |
Value
YAML file with changed parameters.