Subset rows in the taxonomy table or sample data using column values

Source: R/dplyr-verbs.R

These functions are wrappers around dplyr::filter() that make it possible to subset rows (corresponding to taxa or samples) using column values in the taxonomy table or sample data.

filter_tax_table(x, ...)

# S4 method for phyloseq
filter_tax_table(x, ...)

# S4 method for taxonomyTable
filter_tax_table(x, ...)

filter_sample_data(x, ...)

# S4 method for phyloseq
filter_sample_data(x, ...)

# S4 method for sample_data
filter_sample_data(x, ...)

Arguments

x

A phyloseq, taxonomyTable, or sample_data object
...

Expressions passed to dplyr::filter()

Examples

data(GlobalPatterns)

ps <- GlobalPatterns %>%
  filter_tax_table(Kingdom == "Bacteria") %>%
  filter_sample_data(SampleType %in% c("Feces", "Soil"))

#> Error in filter_sample_data(., SampleType %in% c("Feces", "Soil")): could not find function "filter_sample_data"