as.data.frame: get the table of diffAnalysisClass

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

Description

get the table of diffAnalysisClass

Usage

## S3 method for class 'diffAnalysisClass'
as.data.frame(x, ...)

## S3 method for class 'alphasample'
as.data.frame(x, ...)

## S3 method for class 'diffAnalysisClass'
as.data.frame(x, ...)

## S3 method for class 'alphasample'
as.data.frame(x, ...)

Arguments

x	object, diffAnalysisClass
...,	additional parameters

Value

a data.frame contained results of diff_analysis

Examples

data(kostic2012crc)
kostic2012crc
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)
restab <- as.data.frame(diffres)
head(restab)

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.