Update README.md

README.md

@@ -57,15 +57,24 @@ Steps:
 
 1. Fire up emacs
 2. `Alt-x` and `R` gets you an R session
-3. Enter `library(shinyscreen)`
-4. Enter `options(browser="chromium")`
-5. Enter `launch()` 
+3. If asked, set your start working directory, e.g. 
+`setwd('/home/user/Desktop/ISB401/')` 
+(where `user` is an alias for your username)
+4. Enter `library(shinyscreen)`
+5. Enter `options(browser="chromium")`
+6. Enter `launch()` 
+
+To create subdirectories for different Shinyscreen calculations, 
+use `dir.create()` and `setwd()` to create and set new working 
+directories, respectively. This is highly recommended otherwise 
+you will auto-detect and/or overwrite previous results. 
 
 
 Alternatively, there there are two icons on your desktop that will
 start Shinyscreen immediately without a R session. One starts the
 stable version of Shinyscreen (used in this course). The other runs a
 development version (you can try it out if you feel adventurous).
+If you choose this path you are at the mercy of the default file path.
 
 
 ### Material needed for the practical
@@ -77,5 +86,15 @@ The *mzML* data files are in `/mnt/exchange` directory.
 2. Input files for Shinyscreen from [here](https://git-r3lab.uni.lu/eci/isb401/-/tree/master/shinyscreen_files)
 
 
+### Some emacs tips
+To execute a script in Emacs Ess, you have different shortcuts:
+
+1. `Ctrl alt x`: runs a Paragraph
+2. `Ctrl enter`: similar, but closer to Rstudio in how it 
+treats collections of sratements
+3. `Ctrl j`: runs a single line
+
+The above commands are used when you have a separate R script that is 
+being evaluated in the session. In the session itself, it's just enter