Do 16s Data Analysis and Generate Figures

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Documentation for package ‘microbial’ version 0.0.21

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

.checkfile	check file format
.getstar	replace p value with star
.lda.fun	LEfse function
betadiv	calcaute beta diversity
betatest	PERMANOVA test for phyloseq
biomarker	Identify biomarker by using randomForest method
buildTree	contruction of plylogenetic tree (extreme slow)
data-physeq	The physeq data was modified from the (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)
difftest	Calculate differential bacteria with DESeq2
distcolor	distinguish colors for making figures
do_aov	do anova test and return results as data.frame
do_ttest	do t.test
do_wilcox	do wilcox test
glmr	Do the generalized linear model regression
ldamarker	Identify biomarker by using LEfSe method
lightcolor	light colors for making figures
normalize	Normalize the phyloseq object with different methods
otu_table	extract otu table
physeq	The physeq data was modified from the (Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)
phy_tree	Retrieve phylogenetic tree (phylo-class) from object.
plotalpha	plot alpha diversity
plotbar	plot bar for relative abundance for bacteria
plotbeta	plot beta diversity
plotdiff	plot differential results
plotLDA	plot LEfSe results from ldamarker function
plotmarker	plot the biomarker from the biomarker function with randomForest
plotquality	plot the quality for the fastq file
prefilter	filter the phyloseq
preRef	Download the reference database
processSeq	Perform dada2 analysis
psmelt	Melt phyloseq data object into large data.frame
richness	calculat the richness for the phyloseq object
sample_data	extract sample information
subset_samples	Subset the phyloseq based on sample
subset_taxa	Subset species by taxonomic expression
tax_table	extract taxonomy table