keggLibrary: An example of the library mapping name of compounds to their...

In PAPi: Predict metabolic pathway activity based on metabolomics data

Description

keggLibrary is an example of the keggCodes library used by the function addKeggCodes, which automates the substitution of compounds names by KEGG codes. keggLibrary is a data frame containing a list of KEGG compounds codes in the first column and their respective names in the second column.

Usage

data(keggLibrary)

Format

A data frame with 2 columns and n rows, where n is the number of compounds present in the library.

kegg

a list of KEGG codes for the compounds described in the second column.

Name

a list of compound names related to the KEGG codes in column one.

Details

For a high-throughput platform, the keggLibrary must contain all the compounds potentially identifiable by the protocol in use. Every time a new compound is added, for example in the GC-MS library, the same compound must be added to the keggLibrary.

References

Aggio, R.B.M; Ruggiero, K. and Villas-Boas, S.G. (2010) - Pathway Activity Profiling (PAPi): from metabolite profile to metabolic pathway activity. Bioinformatics.

Examples

data(keggLibrary)
print(keggLibrary)

PAPi documentation built on Oct. 31, 2019, 3:19 a.m.