adap.to.rc: adap.to.rc

In cbroeckl/csu.pmf.tools: a collection of features used internally at CSU PMF for non-targeted metabolomics data processing

adap.to.rc

Description

use pubchem rest and view APIs to retreive structures, CIDs (if a name or inchikey is given), synonyms, and optionally vendor data, when available.

Usage

adap.to.rc(
  seq = "seq.csv",
  spec.abund = "signal.csv",
  msp = "spectra.msp",
  annotations = "annotations.xlsx",
  mzdec = 1,
  min.score = 700,
  manual.name = FALSE,
  qc.tag = "qc",
  blank.tag = "blank",
  factor.names = c()
)

Arguments

seq	file name/path to sequence file - expect filenames in column 1 and sample names in column 2. filenames should match those in spec.abund
spec.abund	file name/path to adap-big export of signal intensities. .csv file expected
msp	file name/path to .msp file created by adap-big
annotations	file name/path to annotations .xlsx file. generally 'simple_export.xlsx'
mzdec	mz decimals to report for internal storage/reporting. generally we want 0 for adap kdb
min.score	700 (out of 1000) by default
manual.name	when looking up inchikey/names, should manual input be used to fill ambiguous names? generally recommend TRUE
qc.tag	a character string by which to recognize a sample as a qc sample. i.e. 'QC' or 'qc'.
blank.tag	a character string by which to recognize a sample as a blank sample. i.e. 'blank' or 'Blank'.

Details

useful for moving from chemical name to digital structure represtation. greek letters are assumed to be 'UTF-8' encoded, and are converted to latin text before searching. if you are reading in your compound name list, do so with 'encoding' set to 'UTF-8'.

Value

returns a ramclustR structured object suitable for down stream processing steps.

Author(s)

Corey Broeckling

cbroeckl/csu.pmf.tools documentation built on Jan. 26, 2024, 6:27 p.m.