SummarizedPhyloseq-accessors: Accessors for SummarizedPhyloseq class and...

In zhuchcn/phylox: Analyzing and Visualization Microbiome Data on Different Phylogenic Levels

Description

Accessor methods for the SummarizedPhyloseq-class and the SummarizedPhyloStats-class

Usage

## S4 method for signature 'SummarizedPhyloseq'
kingdom_table(object)

## S4 method for signature 'SummarizedPhyloseq'
phylum_table(object)

## S4 method for signature 'SummarizedPhyloseq'
class_table(object)

## S4 method for signature 'SummarizedPhyloseq'
order_table(object)

## S4 method for signature 'SummarizedPhyloseq'
family_table(object)

## S4 method for signature 'SummarizedPhyloseq'
genus_table(object)

## S4 method for signature 'SummarizedPhyloseq'
species_table(object)

## S4 method for signature 'SummarizedPhyloStats'
kingdom_table(object)

## S4 method for signature 'SummarizedPhyloStats'
phylum_table(object)

## S4 method for signature 'SummarizedPhyloStats'
class_table(object)

## S4 method for signature 'SummarizedPhyloStats'
order_table(object)

## S4 method for signature 'SummarizedPhyloStats'
family_table(object)

## S4 method for signature 'SummarizedPhyloStats'
genus_table(object)

## S4 method for signature 'SummarizedPhyloStats'
species_table(object)

## S4 method for signature 'SummarizedPhyloStats'
otu_table(object)

Arguments

object

Either a SummarizedPhyloseq or SummarziedPhyloStats object.

Details

These methods retrieve slots from either a SummarizedPhyloseq or a SummarizedPhyloStats object.

kingdom_table()

Retrieve the kingdom_table slot

phylum_table()

Retrieve the phylum_table slot

class_table()

Retrieve the class_table slot

order_table()

Retrieve the order_table slot

family_table()

Retrieve the family_table slot

genus_table()

Retrieve the genus_table slot

species_table()

Retrieve the species_table slot

otu_table()

Retrieve the otu_table slot

Value

A otu_table-class object.

Author(s)

Chenghao Zhu

See Also

SummarizedPhyloseq-class SummarizedPhyloStats-class summarizeFromPhyloseq

zhuchcn/phylox documentation built on May 31, 2019, 5:14 p.m.