R: Do 16s Data Analysis and Generate Figures

# Do 16s Data Analysis and Generate Figures

## Documentation for package ‘microbial’ version 0.0.22

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## 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