PAPi-package: Pathway Activity Profiling

In PAPi: Predict metabolic pathway activity based on metabolomics data

Description

PAPi is an R package that implements the PAPi algorithm published in Aggio et al. 2010. It relates metabolite abundances to metabolic pathway activity. For this, PAPi uses a typical metabolomics data set and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database (http://www.genome.jp/kegg/).

Details

Package:	PAPi
Type:	Package
Version:	0.99.3
Date:	2013-03-27
License:	GPL(>= 2)

PAPi has five functions: buildDatabase, addKeggCodes, papi, papiHtest and papiLine. The main function of PAPi is papi, which uses a metabolomics data set for predicting the activity of metabolic pathways. For this, papi requires the name of each compound to be substituted by its respective KEGG code. KEGG code is a unique compound identifier in KEGG database. The function addKeggCodes then automatically substitutes compounds names by their respective KEGG codes while papi generates a list of metabolic pathways with their predicted metabolic activity. papiHtest performs ANOVA or t-test on results generated by papi. Finally, papiLine generates a line graph of results produced by papi or papiHtest.

Author(s)

Raphael Aggio Maintainer: Raphael Aggio ([e-mail])

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

### Building input data ####
Names <- c("Replicates", "C00197", "C05345", "C00031", "C00118", "C00111")
Sample1 <- c("cond1", 0.2, 0.3, 0.8, 1.1, 1.2)
Sample2 <- c("cond1", 0.3, 0.2, 0.6, 1.5, 1.5)
Sample3 <- c("cond1", 0.5, 0.4, 0.7, 1.2, 1.3)
Sample4 <- c("cond2", 1.1, 0.6, 1.2, NA, 0.2)
Sample5 <- c("cond2", 1.0, 0.7, 1.1, NA, 0.3)
Sample6 <- c("cond2", 0.9, 0.7, 1.5, NA, 0.2) 

papiData <- data.frame(cbind(Names, Sample1, Sample2, Sample3, Sample4, Sample5,
Sample6), stringsAsFactors = FALSE)

### Applying papi ####
#papiResults <- papi(papiData, save = FALSE)

Example output

Loading required package: svDialogs
Loading required package: svGUI
Loading required package: KEGGREST

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