Create a new RStudio project

Open RStudio and create a new project, for more info see https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects

Learn more about packrat see https://rstudio.github.io/packrat/

Set some options and make sure the packages edgeR, gplots, RColorBrewer, topGO, KEGGREST, Rgraphviz and org.Hs.eg.db are installed (if not install it), and then load

In the R console run the following commands

if (!any(rownames(installed.packages()) == "edgeR")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("edgeR", version = "3.8")
}
library(edgeR)

## Loading required package: limma

if (!any(rownames(installed.packages()) == "topGO")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("topGO", version = "3.8")
}

## Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)

## Installing package(s) 'topGO'

## also installing the dependencies 'graph', 'SparseM'

## Update old packages: 'BiocParallel', 'caTools', 'class', 'codetools',
##   'dplyr', 'evaluate', 'flexmix', 'forcats', 'formatR', 'GenomeInfoDb',
##   'gplots', 'haven', 'Hmisc', 'igraph', 'irlba', 'knitr', 'later',
##   'Matrix', 'metap', 'mgcv', 'modelr', 'mvtnorm', 'openssl', 'pbapply',
##   'processx', 'proxy', 'purrr', 'R.utils', 'R6', 'RCurl', 'readxl',
##   'reticulate', 'Rsamtools', 'stringi', 'stringr', 'sys', 'tidyr',
##   'vegan', 'xfun'

library(topGO)

## Loading required package: BiocGenerics

## Loading required package: parallel

## 
## Attaching package: 'BiocGenerics'

## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB

## The following object is masked from 'package:limma':
## 
##     plotMA

## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs

## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind,
##     colMeans, colnames, colSums, dirname, do.call, duplicated,
##     eval, evalq, Filter, Find, get, grep, grepl, intersect,
##     is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
##     paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
##     Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
##     table, tapply, union, unique, unsplit, which, which.max,
##     which.min

## Loading required package: graph

## Loading required package: Biobase

## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.

## Loading required package: GO.db

## Loading required package: AnnotationDbi

## Loading required package: stats4

## Loading required package: IRanges

## Loading required package: S4Vectors

## 
## Attaching package: 'S4Vectors'

## The following object is masked from 'package:base':
## 
##     expand.grid

## 

## Loading required package: SparseM

## 
## Attaching package: 'SparseM'

## The following object is masked from 'package:base':
## 
##     backsolve

## 
## groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

## 
## Attaching package: 'topGO'

## The following object is masked from 'package:IRanges':
## 
##     members

if (!any(rownames(installed.packages()) == "KEGGREST")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("KEGGREST", version = "3.8")
}

## Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)

## Installing package(s) 'KEGGREST'

## Update old packages: 'BiocParallel', 'caTools', 'class', 'codetools',
##   'dplyr', 'evaluate', 'flexmix', 'forcats', 'formatR', 'GenomeInfoDb',
##   'gplots', 'haven', 'Hmisc', 'igraph', 'irlba', 'knitr', 'later',
##   'Matrix', 'metap', 'mgcv', 'modelr', 'mvtnorm', 'openssl', 'pbapply',
##   'processx', 'proxy', 'purrr', 'R.utils', 'R6', 'RCurl', 'readxl',
##   'reticulate', 'Rsamtools', 'stringi', 'stringr', 'sys', 'tidyr',
##   'vegan', 'xfun'

library(KEGGREST)

if (!any(rownames(installed.packages()) == "Rgraphviz")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("Rgraphviz", version = "3.8")
}

## Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)

## Installing package(s) 'Rgraphviz'

## Update old packages: 'BiocParallel', 'caTools', 'class', 'codetools',
##   'dplyr', 'evaluate', 'flexmix', 'forcats', 'formatR', 'GenomeInfoDb',
##   'gplots', 'haven', 'Hmisc', 'igraph', 'irlba', 'knitr', 'later',
##   'Matrix', 'metap', 'mgcv', 'modelr', 'mvtnorm', 'openssl', 'pbapply',
##   'processx', 'proxy', 'purrr', 'R.utils', 'R6', 'RCurl', 'readxl',
##   'reticulate', 'Rsamtools', 'stringi', 'stringr', 'sys', 'tidyr',
##   'vegan', 'xfun'

library(Rgraphviz)

## Loading required package: grid

## 
## Attaching package: 'grid'

## The following object is masked from 'package:topGO':
## 
##     depth

## 
## Attaching package: 'Rgraphviz'

## The following objects are masked from 'package:IRanges':
## 
##     from, to

## The following objects are masked from 'package:S4Vectors':
## 
##     from, to

if (!any(rownames(installed.packages()) == "org.Hs.eg.db")){
  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install("org.Hs.eg.db", version = "3.8")
}

## Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.2 (2018-12-20)

## Installing package(s) 'org.Hs.eg.db'

## installing the source package 'org.Hs.eg.db'

## Update old packages: 'BiocParallel', 'caTools', 'class', 'codetools',
##   'dplyr', 'evaluate', 'flexmix', 'forcats', 'formatR', 'GenomeInfoDb',
##   'gplots', 'haven', 'Hmisc', 'igraph', 'irlba', 'knitr', 'later',
##   'Matrix', 'metap', 'mgcv', 'modelr', 'mvtnorm', 'openssl', 'pbapply',
##   'processx', 'proxy', 'purrr', 'R.utils', 'R6', 'RCurl', 'readxl',
##   'reticulate', 'Rsamtools', 'stringi', 'stringr', 'sys', 'tidyr',
##   'vegan', 'xfun'

library(org.Hs.eg.db)

## 

library(edgeR)
if (!any(rownames(installed.packages()) == "gplots")){
install.packages("gplots")
}
library(gplots)

## 
## Attaching package: 'gplots'

## The following object is masked from 'package:IRanges':
## 
##     space

## The following object is masked from 'package:S4Vectors':
## 
##     space

## The following object is masked from 'package:stats':
## 
##     lowess

if (!any(rownames(installed.packages()) == "RColorBrewer")){
install.packages("RColorBrewer")
}
library(RColorBrewer)

Download the template Markdown workshop document and open it

In the R console run the following command

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2019_March_UCSF_mRNAseq_Workshop/master/differential_expression/DE_Analysis.Rmd", "DE_Analysis.Rmd")

Download the data file for the workshop document and preview/open it

This is the the counts file generated after running Generating Summarized Counts. I’ve also uploaded to the github pages

In the R console run the following command.

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2019_March_UCSF_mRNAseq_Workshop/master/differential_expression/de_data/rnaseq_workshop_counts.txt", "rnaseq_workshop_counts.txt")

Edit the file YAML portion

The top YAML (YAML ain’t markup language) portion of the doc tells RStudio how to parse the document.

---
title: "Data_in_R"
author: your_name
date: current_date
output:
    html_notebook: default
    html_document: default
---