DAVID: Human longitudinal microbiome data

In themetagenomics: Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data

Description

This includes 16S amplicon sequencing measurements over time from 2 individuals. One donor provided both gut and oral samples, whereas the other donor provided only gut samples. The abundance table was generated via Dada2 using the Silva reference database. The data span 350 time points.

Usage

DAVID

Format

A list containing a 746x1493 matrix (ABUND), a 1493x7 matrix (TAX), and a 746x9 dataframe (META).

Source

BioProject: PRJEB6518 (PubMed)

References

David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., Erdman, S. E., and Alm, E. J. (2014). Genome Biology. 15:R89.

Examples

hist(log(DAVID$ABUND + 1),100)
table(DAVID$META$Site,DAVID$META$Donor)

Example output

Loading required package: Rcpp
               
                2202:DonorA 2202:DonorB
  UBERON:feces          312         176
  UBERON:saliva         258           0

themetagenomics documentation built on May 1, 2020, 1:06 a.m.