The lineages for OTUs in David data stool subject A and B. The first column holds the OTU, column 2 to 8 hold the domain, phylum, class, order, family, genus and species level classification and column 9 holds the lineage ending with the OTU. If the OTU has not been classified to a given taxonomic level, the entry for it is "none".
data(david_stool_lineages)
a matrix with 5431 rows representing OTUs and 10 columns representing taxonomic information
David et al. (2014) Host lifestyle affects human microbiota on daily timescales Genome Biology vol. 15 (7):R89 Genome Biology
# list the families with most OTUs in the David stool data rev(sort(table(david_stool_lineages[,6])))[1:10]#> #> Lachnospiraceae Ruminococcaceae none Enterobacteriaceae #> 1752 661 552 148 #> Comamonadaceae Bacillaceae Bacteroidaceae Streptococcaceae #> 118 100 86 84 #> Sphingomonadaceae Flavobacteriaceae #> 76 76# get the genus of the top abundant OTU in the stool A data set data(david_stoolA_otus) sorted=sort(apply(david_stoolA_otus,1,sum),index.return=TRUE, decreasing=TRUE) index=which(david_stool_lineages[,1]==rownames(david_stoolA_otus)[sorted$ix[1]]) david_stool_lineages[index,7]#> [1] Faecalibacterium #> 434 Levels: Abiotrophia Achromobacter Acidaminococcus ... u114