Caporaso Stool Sequencing Data for Subject M3 on level 6

Source: R/caporaso_M3FecesL6.R

Mostly genus-level counts (L6) from stool samples of subject M3 over time.

data(caporaso_M3FecesL6)

Format

An object of class data.frame with 335 rows and 332 columns.

Value

TaxonxSample matrix of size 335 x 332

Details

Subject M3 was followed for 15 months. V4 16S region was sequenced. A counter was attached to genera appearing more than once in the count table.

References

Caporaso et al. (2011) Moving pictures of the human microbiome Genome Biology vol. 12:R50 Genome Biology

Examples

data(caporaso_M3FecesL6)
# sort taxa by abundance and print top 10 most abundant taxa
sorted <- sort(apply(caporaso_M3FecesL6,1,sum),decreasing = TRUE, index.return = TRUE)
rownames(caporaso_M3FecesL6)[sorted$ix[1:10]]
#>  [1] "Bacteroides"      "Faecalibacterium" "Parabacteroides"  "Ruminococcaceae" 
#>  [5] "Bacteroidales"    "Lachnospiraceae"  "Roseburia"        "Alistipes"       
#>  [9] "Prevotella"       "Ruminococcus2"