Caporaso Tongue Sequencing Data for Subject F4 on level 6

Source: R/caporaso_F4TongueL6.R

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

data(caporaso_F4TongueL6)

Format

An object of class data.frame with 373 rows and 135 columns.

Value

TaxonxSample matrix of size 373 x 135

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_F4TongueL6)
# sort taxa by abundance and print top 10 most abundant taxa
sorted <- sort(apply(caporaso_F4TongueL6,1,sum),decreasing = TRUE, index.return = TRUE)
rownames(caporaso_F4TongueL6)[sorted$ix[1:10]]
#>  [1] "Streptococcus"   "Prevotella"      "Neisseria"       "Veillonella"    
#>  [5] "Pasteurellaceae" "Rothia"          "Haemophilus"     "Fusobacterium"  
#>  [9] "Actinomyces"     "Granulicatella"