export.msfinder

export pubchem.bio pc.bio syle data.table to format suitable for MSFinder input.

All 'PubChem' compounds are downloaded to a local computer, but for each compound, only partial records are used.  The data are organized into small files referenced by 'PubChem' CID.  This package also contains functions to parse the biologically relevant compounds from all 'PubChem' compounds, using biological database sources, pathway presence, and taxonomic relationships. Taxonomy is used to generate a lowest common ancestor taxonomy ID (NCBI) for each biological metabolite, which then enables creation of taxonomically specific metabolome databases for any taxon.

Corey Broeckling

pubchem.bio

Biologically Informed Metabolomic Libraries from 'PubChem'

export.msfinder function

<dl><dt>pc.bio.object</dt>
<dd>input data.table, generated from 'build.pubchem.bio' or 'build.taxon.metabolome' functions</dd>
<dt>export.file.name</dt>
<dd>valid file path and name. Extension should be listed as '.tsv'.</dd></dl>

Arguments

Author

export.msfinder — export.msfinder

<dl>

<dt>pc.bio.object</dt>
<dd>input data.table, generated from 'build.pubchem.bio' or 'build.taxon.metabolome' functions</dd>


<dt>export.file.name</dt>
<dd>valid file path and name. Extension should be listed as '.tsv'.</dd>

</dl>

export.msfinder: export.msfinder

Description

Usage

Value

Arguments

Author

Details