MPSE-accessors: MPSE accessors

In xiangpin/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

MPSE accessors

Description

MPSE accessors

Usage

## S4 method for signature 'MPSE,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

## S4 replacement method for signature 'MPSE,DataFrame'
colData(x, ...) <- value

## S4 replacement method for signature 'MPSE,NULL'
colData(x, ...) <- value

tax_table(object)

## S4 method for signature 'MPSE'
tax_table(object)

## S4 method for signature 'tbl_mpse'
tax_table(object)

## S4 method for signature 'grouped_df_mpse'
tax_table(object)

otutree(x, ...)

## S4 method for signature 'MPSE'
otutree(x, ...)

## S4 method for signature 'tbl_mpse'
otutree(x, ...)

## S4 method for signature 'MPSE'
otutree(x, ...)

otutree(x, ...) <- value

## S4 replacement method for signature 'MPSE,treedata'
otutree(x, ...) <- value

## S4 replacement method for signature 'MPSE,phylo'
otutree(x, ...) <- value

## S4 replacement method for signature 'MPSE,NULL'
otutree(x, ...) <- value

## S4 replacement method for signature 'tbl_mpse,treedata'
otutree(x, ...) <- value

## S4 replacement method for signature 'grouped_df_mpse,treedata'
otutree(x, ...) <- value

## S4 replacement method for signature 'tbl_mpse,NULL'
otutree(x, ...) <- value

## S4 replacement method for signature 'grouped_df_mpse,NULL'
otutree(x, ...) <- value

taxatree(x, ...)

## S4 method for signature 'MPSE'
taxatree(x, ...)

## S4 method for signature 'tbl_mpse'
taxatree(x, ...)

## S4 method for signature 'grouped_df_mpse'
taxatree(x, ...)

taxatree(x, ...) <- value

## S4 replacement method for signature 'MPSE,treedata'
taxatree(x, ...) <- value

## S4 replacement method for signature 'MPSE,NULL'
taxatree(x, ...) <- value

## S4 replacement method for signature 'tbl_mpse,treedata'
taxatree(x, ...) <- value

## S4 replacement method for signature 'tbl_mpse,NULL'
taxatree(x, ...) <- value

## S4 replacement method for signature 'grouped_df_mpse,treedata'
taxatree(x, ...) <- value

## S4 replacement method for signature 'grouped_df_mpse,NULL'
taxatree(x, ...) <- value

taxonomy(x, ...) <- value

## S4 replacement method for signature 'MPSE,data.frame'
taxonomy(x, ...) <- value

## S4 replacement method for signature 'MPSE,matrix'
taxonomy(x, ...) <- value

## S4 replacement method for signature 'MPSE,taxonomyTable'
taxonomy(x, ...) <- value

## S4 replacement method for signature 'MPSE,NULL'
taxonomy(x, ...) <- value

refsequence(x, ...)

## S4 method for signature 'MPSE'
refsequence(x, ...)

refsequence(x, ...) <- value

## S4 replacement method for signature 'MPSE,XStringSet'
refsequence(x, ...) <- value

## S4 replacement method for signature 'MPSE,NULL'
refsequence(x, ...) <- value

## S4 replacement method for signature 'MPSE'
rownames(x) <- value

Arguments

x	MPSE object
i, j, ...	Indices specifying elements to extract or replace. Indices are 'numeric' or 'character' vectors or empty (missing) or NULL. Numeric values are coerced to integer as by 'as.integer' (and hence truncated towards zero). Character vectors will be matched to the 'names' of the object (or for matrices/arrays, the 'dimnames')
drop	logical If 'TRUE' the result is coerced to the lowest possible dimension (see the examples). This only works for extracting elements, not for the replacement.
value	XStringSet object or NULL
object	parameter of tax_table, R object, MPSE class in here.

Value

taxonomyTable class

xiangpin/MicrobiotaProcess documentation built on Nov. 12, 2024, 2:05 p.m.