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Tutorials for R

Author : Daniel VAULOT
UMR 7144 CNRS-UPMC, Station Biologique, Place G. Tessier, 29680 Roscoff FRANCE
email: [email protected] / [email protected]

I have posted here a few tutorials for different types of analysis of microbial communities. For each of these of these tutorials there is a detailed explanation created with Rmd (see below).

Please post any question or issues here : https://github.com/vaulot/R_tutorials/issues

Prerequisites to be installed to run these tutorials

  • Download from GitHub the whole set of tutorial

  • Unzip the files to a folder on your computer

  • Install R

  • Install R studio

  • Download this set tutorial from GitHub : R tutorials

  • Download and install the following libraries by running under R studio the following lines

install.packages("dplyr")     # To manipulate dataframes
install.packages("tidyr")     # To manipulate dataframes
install.packages("readxl")    # To read Excel files into R
install.packages("ggplot2")   # for high quality graphics
install.packages("maps")      # to make maps
install.packages("gridExtra") # for grids
install.packages("treemap")   # for treemaps
install.packages("FactoMineR") # multivariate analysis
install.packages("plotrix" )  # needed for standard error

source("https://bioconductor.org/biocLite.R")
biocLite('phyloseq')          # metabarcode data analysis
biocLite("Biostrings")        # manipulate sequences

Step by step instructions

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r_tutorials's Issues

R tutorials transformation

Hi, I am just going through your R tutorials, which are very useful to learn phyloseq package.
One question I have is about the transformation of the read into relative data.

Why do you choose the median sum and not 100 or the minimum of all samples ?

total = median(sample_sums(carbom))
  standf = function(x, t=total) round(t * (x / sum(x)))
  carbom = transform_sample_counts(carbom, standf)

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