Caporaso Stool Sequencing Data for Subject F4 on level 6

Source: R/caporaso_F4FecesL6.R

Mostly genus-level counts (L6) from stool samples of subject F4 over time.

data(caporaso_F4FecesL6)

Format

An object of class data.frame with 335 rows and 130 columns.

Value

TaxonxSample matrix of size 335 x 130

Details

Subject F4 was followed over 6 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_F4FecesL6)
# sort taxa by abundance and print top 10 most abundant taxa
sorted <- sort(apply(caporaso_F4FecesL6,1,sum),decreasing = TRUE, index.return = TRUE)
rownames(caporaso_F4FecesL6)[sorted$ix[1:10]]
#>  [1] "Bacteroides"           "Akkermansia"           "Faecalibacterium"     
#>  [4] "Lachnospira"           "Lachnospiraceae"       "Roseburia"            
#>  [7] "Phascolarctobacterium" "Clostridium2"          "Bacteroidales"        
#> [10] "Escherichia"