exptable: Sample table for the generation of a database of standards...
In metaMS: MS-based metabolomics annotation pipeline
Description
Usage
Format
Details
Author(s)
See Also
Description
An example of a table used to construct a database of
standards. This particular table is used to obtain object LCDBtest.
Usage
1
Format
exptable is a data.frame summarizing information on the
chemical standards used for creating a database.
Column description:
- ChemSpiderID
The Chemspider ID of a specific compound.
- compound
A string containing the (human) readable name of the
compound.
- formula
The formula of the compound.
- M.ref
The theoretical value for the observed m/z reference
ion. This can be, for example, the protonated (de-protonated) molecular
ion, a known adduct or a characteristic fragment.
- mz.observed
The manually validated m/z value of the reference
ion.
- RTman
The manually validated retention time value for the standard.
- stdFile
The name (including the path) of the raw data file of the
standard.
Details
Mandatory fields are: ChemSpiderID, mz.observed,
RTman, and stdFile.
In the current implementation the M.ref value is not used in the
creation of the DB. The difference between M.ref and
m.observed, however, could be used to construct the mass error
surface used during feature annotation.
The sample table is also an element (Reftable) of the LCDB list
generated by createSTDdbLC.
Author(s)
Pietro Franceschi
See Also
metaMS documentation built on Nov. 8, 2020, 8:21 p.m.
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Description Usage Format Details Author(s) See Also
Description
An example of a table used to construct a database of
standards. This particular table is used to obtain object LCDBtest.
Usage
1 |
Format
exptable is a data.frame summarizing information on the
chemical standards used for creating a database.
Column description:
- ChemSpiderID
The Chemspider ID of a specific compound.
- compound
A string containing the (human) readable name of the compound.
- formula
The formula of the compound.
- M.ref
The theoretical value for the observed m/z reference ion. This can be, for example, the protonated (de-protonated) molecular ion, a known adduct or a characteristic fragment.
- mz.observed
The manually validated m/z value of the reference ion.
- RTman
The manually validated retention time value for the standard.
- stdFile
The name (including the path) of the raw data file of the standard.
Details
Mandatory fields are: ChemSpiderID, mz.observed,
RTman, and stdFile.
In the current implementation the M.ref value is not used in the
creation of the DB. The difference between M.ref and
m.observed, however, could be used to construct the mass error
surface used during feature annotation.
The sample table is also an element (Reftable) of the LCDB list
generated by createSTDdbLC.
Author(s)
Pietro Franceschi
See Also
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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