R script for metagenomics

mdires.R

## mdires.R

## 1.
library(ebimetagenomics)
ps = getProjectSummary("SRP066323")
samples = projectSamples(ps)
otu1 = getSampleOtu(ps,samples[1])
otu2 = getSampleOtu(ps,samples[2])

## 2.
plotOtu(otu1)
plotOtu(otu2)

## 3.
dim(otu1)[1]
dim(otu2)[1]

## 4.
sum(otu1$Count)
sum(otu2$Count)

## 5.
library(vegan)
estimateR(otu1$Count)
estimateR(otu2$Count)

library(breakaway)
breakaway(convertOtuTad(otu1))
breakaway(convertOtuTad(otu2))

breakaway_nof1(convertOtuTad(otu1)[-1,])
breakaway_nof1(convertOtuTad(otu2)[-1,])

## 6.
fitsad(otu1$Count,"lnorm")
fitsad(otu1$Count,"poilog")
fitsad(otu1$Count,"ls")
fitsad(otu1$Count,"mzsm")

fitsad(otu2$Count,"lnorm")
fitsad(otu2$Count,"poilog")
fitsad(otu2$Count,"ls")
fitsad(otu2$Count,"mzsm")

## eof