show-methods: method extensions to show for diffAnalysisClass or...

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

method extensions to show for diffAnalysisClass or alphasample objects.

Description

method extensions to show for diffAnalysisClass or alphasample objects.

Usage

## S4 method for signature 'diffAnalysisClass'
show(object)

## S4 method for signature 'alphasample'
show(object)

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

Arguments

object

object, diffAnalysisClass or alphasample class

Value

print info

Author(s)

Shuangbin Xu

Examples

## Not run: 
data(kostic2012crc)
kostic2012crc %<>% as.phyloseq()
head(phyloseq::sample_data(kostic2012crc),3)
kostic2012crc <- phyloseq::rarefy_even_depth(kostic2012crc,rngseed=1024)
table(phyloseq::sample_data(kostic2012crc)$DIAGNOSIS)
set.seed(1024)
diffres <- diff_analysis(kostic2012crc, classgroup="DIAGNOSIS",
                        mlfun="lda", filtermod="fdr",
                        firstcomfun = "kruskal.test",
                        firstalpha=0.05, strictmod=TRUE, 
                        secondcomfun = "wilcox.test",
                        subclmin=3, subclwilc=TRUE,
                        secondalpha=0.01, lda=3)
show(diffres)

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.