The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.
The package includes:
1. Relative Abundance plots (Stacked Bar Plot, Heatmap) 2. Diversity plots (Alpha and Beta diversity, Exploratory Tree, BiPlot, Co-Occurrence) 3. Differential Expression (Expression Plots, Limma) 4. Confidence Region Plots 5. PCA plots 6. PCoA plots 7. Alluvial Plots for longitudinal data 8. Core OTU analysis
runPathoStat is the pipeline function that generates the PathoStat report
and launches shiny app when in interactive mode. It combines all the functions
into one step.
To begin, install Bioconductor and simply run the following to automatically install PathoStat and all the dependencies, except pandoc, which you have to manually install as follows.
Install 'pandoc' package by following the instructions at the following URL: http://pandoc.org/installing.html
Rstudio also provides pandoc binaries at the following location for Windows, Linux and Mac: https://s3.amazonaws.com/rstudio-buildtools/pandoc-1.13.1.zip
If you want to install the latest development version of PathoStat from Github, use devtools to install it as follows:
require(devtools) install_github("mani2012/PathoStat", build_vignettes=TRUE)
If you want to manually install the PathoStat dependencies, run the following:
source("http://bioconductor.org/biocLite.R") biocLite(c('MCMCpack', 'limma', 'corpcor', 'rmarkdown', 'knitr', 'pander', 'matrixStats', 'reshape2', 'scales', 'ggplot2', 'rentrez', 'BatchQC', 'DT', 'gtools', 'plyr', 'tidyr', 'dplyr', 'ape', 'phyloseq', 'shiny', 'grDevices', 'stats', 'methods', 'XML', 'graphics', 'utils', 'alluvial', 'BiocStyle'))
If all went well you should now be able to load PathoStat:
require(PathoStat) vignette('PathoStatIntro', package='PathoStat') vignette("PathoStatUserManual", package='PathoStat') vignette("PathoStatAdvanced", package='PathoStat') runPathoStat()
If you are having issues with the installation, you may have to setup local directory, if you do not have permissions to install in the default location for R. You may also want to load a version of R 3.3.1 or higher.
export R_LIBS="/my_own_local_directory/R_libs" module load R/R-3.2.4
And do something like the following
install.packages("devtools", repos="http://cran.r-project.org", lib="/my_own_local_directory/R_libs")
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