Utility to join otu_table and tax_table to tibble.
join_otu_tax(x, column_id = "OTUID")phyloseq-class object
Provide name for the column which will hold the rownames of slot.
A tibble
library(microbiomeutilities)
data("zackular2014")
p0 <- zackular2014
otu_tax <- join_otu_tax(p0,column_id = "OTUID")
head(otu_tax)
#> # A tibble: 6 × 96
#> OTUID Domain Phylum Class Order Family Genus Species Adeno…¹ Adeno…² Adeno…³
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <int> <int> <int>
#> 1 d__den… k__Ba… p__Ba… c__B… o__B… f__Ba… g__B… s__ 0 0 0
#> 2 d__den… k__Ba… p__Ba… c__B… o__B… f__Ba… g__B… s__ 0 0 0
#> 3 d__den… k__Ba… p__Fi… c__C… o__C… f__Ru… g__ s__ 0 0 3
#> 4 d__den… k__Ba… p__Ba… c__B… o__B… f__Ba… g__B… s__ 0 0 0
#> 5 d__den… k__Ba… p__Fi… c__C… o__C… f__La… g__B… s__ 1 0 1
#> 6 d__den… k__Ba… p__Ba… c__B… o__B… f__Ba… g__B… s__ 0 1 0
#> # … with 85 more variables: `Adenoma14-2817` <int>, `Adenoma15-2847` <int>,
#> # `Adenoma16-2873` <int>, `Adenoma17-2937` <int>, `Adenoma18-2967` <int>,
#> # `Adenoma19-2971` <int>, `Adenoma20-2995` <int>, `Adenoma21-3129` <int>,
#> # `Adenoma2-2113` <int>, `Adenoma22-3133` <int>, `Adenoma23-3141` <int>,
#> # `Adenoma24-3217` <int>, `Adenoma25-3273` <int>, `Adenoma26-3373` <int>,
#> # `Adenoma27-3379` <int>, `Adenoma28-3391` <int>, `Adenoma29-3399` <int>,
#> # `Adenoma30-3509` <int>, `Adenoma3-2123` <int>, `Adenoma4-2143` <int>, …