Predict metabolic pathway activity based on metabolomics data


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Documentation for package ‘PAPi’ version 1.20.0

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PAPi-package Pathway Activity Profiling
addKeggCodes In a data frame, it substitutes the name of compounds by their respective KEGG codes.
buildDatabase Build a local database containing the required information from KEGG (Kyoto Encyclopedia of Genes and Genomes) database.
keggLibrary An example of the library mapping name of compounds to their respective KEGG codes.
metabolomicsData An example of metabolomics data set used by 'addKeggCodes'.
PAPi Pathway Activity Profiling
papi papi - Pathway Activity Profiling
papiData An example of the data frame produced by 'addKeggCodes' and used by 'papi'.
papiHtest Apply ANOVA or t-test to results produced by 'papi'.
papiLine papiLine generates a line graph of results obtained using 'papi' or 'papiHtest'.
papiResults An example of the data frame produced by 'papi'.