marker_table-methods: Build or access the marker_table

In HuaZou/MicrobiomeAnalysis: Data analysis toolkits in metagenomics

Build or access the marker_table

Description

This is the recommended function for both building and accessing microbiome marker table (marker_table).

Usage

marker_table(object)

## S4 method for signature 'data.frame'
marker_table(object)

## S4 method for signature 'microbiomeMarker'
marker_table(object)

Arguments

object

an object among the set of classes defined by the microbiomeMarker package that contain marker_table

Value

a marker_table object.

Examples

data(enterotypes_arumugam)
mm <- run_limma_voom(
    enterotypes_arumugam,
    "Enterotype",
    contrast = c("Enterotype 3", "Enterotype 2"),
    pvalue_cutoff = 0.05,
    p_adjust = "fdr"
)
marker_table(mm)

HuaZou/MicrobiomeAnalysis documentation built on May 13, 2024, 11:10 a.m.