filter-phyloseq: Subset rows in the taxonomy table or sample data using column...

In mikemc/speedyseq: Faster implementations of phyloseq functions

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

Description

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.

Usage

filter_tax_table(x, ...)

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

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

filter_sample_data(x, ...)

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

## S4 method for signature '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"))

mikemc/speedyseq documentation built on April 22, 2024, 6:40 p.m.