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@@ -1,12 +1,13 @@
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---
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-title: "RNA-seq study of cynomolgus monkey mesenchymal stem cells treated with interferon gamma"
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+title: RNA-seq study of cynomolgus monkey mesenchymal stem cells treated with interferon
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+ gamma
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author: "Ryan C. Thompson"
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date: "May 8, 2018"
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output:
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- html_document:
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- fig_caption: true
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+ html_notebook:
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+ fig_caption: yes
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pdf_document:
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- fig_caption: true
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+ fig_caption: yes
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---
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```{r setup, include=FALSE}
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@@ -37,13 +38,14 @@ Control and IFNg samples.
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First, let's install all the packages we'll need.
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```{r install_pkgs, eval=FALSE}
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-needed_packages <- c("edgeR", "limma", "SummarizedExperiment", "ggplot2", "locfit", "dplyr", "statmod")
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+if (!requireNamespace("BiocManager", quietly = TRUE))
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+ install.packages("BiocManager")
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already_installed_packages <- rownames(installed.packages())
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+needed_packages <- c("edgeR", "limma", "SummarizedExperiment", "ggplot2", "locfit", "dplyr", "statmod")
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need_to_install <- setdiff(needed_packages, already_installed_packages)
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if (length(need_to_install) > 0) {
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## http://bioconductor.org/install/
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- source("https://bioconductor.org/biocLite.R")
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- biocLite(need_to_install)
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+ BiocManager::install(need_to_install)
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}
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```
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@@ -64,7 +66,7 @@ reads a single R object from a file and returns it. We assign the
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result to a variable.
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```{r loading_data}
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-sexp <- readRDS(gzcon(url("https://www.dropbox.com/s/4lx6q9fgyz66rky/Cyno-RNASeq-SummarizedExperiment.RDS?dl=1")))
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+sexp <- readRDS(gzcon(url("https://darwinawardwinner.github.io/resume/examples/Salomon/Teaching/Cyno-RNASeq-SummarizedExperiment.RDS")))
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print(sexp)
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```
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