psadd: Additions to phyloseq package for microbiome analysis

Description Usage Arguments Details Value Examples

Generate taxa/OTU statistics to compare control samples with the remaining dataset

1	ctrl_samples_stats(physeq, physeq_ctrl)

`physeq`	`otu_table-class`, or `phyloseq-class`
`physeq_ctrl`	`otu_table-class`, or `phyloseq-class` of control sample. It can be the output of `subset_samples_no_zero` for example.

The taxa/OTU prevalence is defined as the number of samples in which it occurs. The prevalence is corrected by substracting the number of samples in the physeq_ctrl object (usually 1).

A data.frame with the following components

RA_In_Ctrl: Taxa/OTU relative abundance in Control sample
RA_In_All: Same Taxa/OTU relative abundance in all samples but Control samples
Ratio: Ratio of RA_In_Ctrl/RA_In_All
Prevalence: Taxa/OTU Prevalence in all samples but Control samples. Range from 0 to the number of samples in physeq object (obtained by ntaxa)

require(phyloseq)
data(soilrep)
# Subset a sample
soilrep.6CC<-subset_samples_no_zero(soilrep, Sample=="6CC")
# Check
ctrl_df<-ctrl_samples_stats(soilrep,soilrep.6CC)
head(ctrl_df)