import.adap.kdb: import.adap.kdb

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

import.adap.kdb

Description

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

Usage

import.adap.kdb(
  ramclustObj = NULL,
  annotations = NULL,
  min.score = 700,
  annotate = TRUE,
  manual.name = TRUE
)

Arguments

ramclustObj	ramclustR object to be annotated.
annotations	file name/path to annotations .xlsx file. generally 'simple_export.xlsx'
min.score	700 (out of 1000) by default
annotate	logical. TRUE by default. for now please leave default
manual.name	when looking up inchikey/names, should manual input be used to fill ambiguous names? generally recommend TRUE

Details

useful for moving from chemical name to digital structure representation. 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.