david_stool_lineages: David et al. stool OTU lineages

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

David et al. stool OTU lineages

Description

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".

Usage

data(david_stool_lineages)

Format

a matrix with 5431 rows representing OTUs and 10 columns representing taxonomic information

References

David et al. (2014) Host lifestyle affects human microbiota on daily timescales Genome Biology vol. 15 (7):R89 Genome Biology

Examples

# list the families with most OTUs in the David stool data
rev(sort(table(david_stool_lineages[,6])))[1:10]
# 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]

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.