kegg.12 {metamicrobiomeR}

Pathway abundance data.

Description

KEGG pathway abundance data from PICRUSt analysis. This is monthly longitudinal data of 50 infants from birth to 2 years of life.

Usage

data(kegg.12)

Format

A list of 2 dataframes for level 1 and level 2 of KEGG pathways.

Source

Gordon Lab

References

Subramanian et al. Nature. 2014 Jun 19; 510(7505): 417–421. (PubMed)

Examples

data(kegg.12)
# Load covariate data
data(covar.rm)
# Comparison of pathway relative abundances for some first pathways of level 1 only
# and assuming crosssectional data (to save running time)
path1<-pathway.compare(pathtab=list(kegg.12[[1]][, 1:2]),
mapfile=covar.rm,sampleid="sampleid",pathsum="rel", stat.med="gamlss",
comvar="gender",adjustvar=c("age.sample","bf"), longitudinal="no",
p.adjust.method="fdr", percent.filter=0.05,relabund.filter=0.00005)
taxcomtab.show(taxcomtab=path1$l1, sumvar="path",tax.lev="l2",
tax.select="none", showvar="genderMale", p.adjust.method="fdr",p.cutoff=1)