rnaQuant

RNA quantification from tissue sections.

Contents

• Required Packages
• Data input
• Visualize RNA integrity data
• Session info

---

Required Packages

Install and load the following R packages before running the reproducible scripts:

# Required packages
lib_List <- c("dplyr", "ggplot2", "grid", "scales")

# Install missing packages
instpack <- lib_List %in% installed.packages()[,"Package"]
if (any(instpack == FALSE)) {
  install.packages(lib_List[!instpack])
}

# Load packages
invisible(lapply(lib_List, library, character.only = TRUE))

---

Data input

Download and extract the rnaQuant repository to the working directory on your computer. Then, set the path for input and output files and source the R scripts:

in_dir <- file.path("rnaQuant-master", "data")
out_dir <- file.path("rnaQuant-master")
path_to_R_files <- file.path("rnaQuant-master", "R")

# Source R files
sourceDir <- function(path, trace = TRUE, ...) {
   for (nm in list.files(path, pattern = "[.][RrSsQq]$")) {
      if(trace) cat(nm,":")
      source(file.path(path, nm), ...)
      if(trace) cat("\n")
   }
}
 
sourceDir(path_to_R_files)

---

Visualize RNA integrity data

... describe data processing and visualization here...

• plotRIN(temp, ...)

Arguments
temp	Indicates data set (embedding temperature). Can be either "56" or "62".

To reproduce the results of this study, execute the following function calls:

plotRIN(temp = "62")
plotRIN(temp = "56")

Session info