modmetabo: Modules for metabolic profiling

In tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Modules for metabolic profiling

Description

Feature and data sets for metabolic profiling

Details

The module set "modmetabo" can be used with tmod to analyse metabolic profiling data. The clusters defined in this set are based on hierarchical clustering of metabolic compounds from human serum and have been published in a paper on metabolic profiling in tuberculosis by Weiner et al. (2012).

For an example analysis, "tbmprof" is a data set containing metabolic profiles of serum isolated from tuberculosis (TB) patients and healthy individuals. The tbmprof is a data frame containing observations in rows and metabolite id's (corresponding to the id's in the modmetabo object). See examples below.

References

Weiner 3rd J, Parida SK, Maertzdorf J, Black GF, Repsilber D, Telaar A, Mohney RP, Arndt-Sullivan C, Ganoza CA, Fae KC, Walzl G. Biomarkers of inflammation, immunosuppression and stress are revealed by metabolomic profiling of tuberculosis patients. PloS one. 2012 Jul 23;7(7):e40221.

See Also

tmod-data

Examples

data(modmetabo)  # module definitions
data(tbmprof)    # example data set
ids <- rownames(tbmprof)
tb  <- factor(gsub("\\..*", "", ids))

## use Wilcoxon test to calculate significant differences
wcx <- apply(tbmprof, 2, function(x) wilcox.test(x ~ tb)$p.value)
wcx <- sort(wcx)
tmodCERNOtest(names(wcx), mset=modmetabo)

tmod documentation built on March 31, 2023, 9 p.m.