# Predict metabolic pathway activity based on metabolomics data

## Documentation for package ‘PAPi’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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'.