Mount Google Drive to Google Colab


We often need to read some data files into R, and it is a bit tricky with google colab as it doesn't have access to the files saved in your local drive. 

The solution is to upload the date files to your google drive. I highly recommend you open a new google account designated for this class only (or your other school work) so that they don't get mixed up with your personal stuff. 

We still need to take a few extra steps, but fortunately I believe that you only need to do this once, or once a while. 

Here is the tricky part. Although we only want to use R, we need to run some Python code first to mount google drive.

First make sure that you change the runtime to Python 3, then run the code below, 

from google.colab import drive
drive.mount('/content/drive')

A new browser window will pop up and ask you for permission to access google drive. Click on the top box to gives google colab the full access. 

Then run the line below, also under the python

load_ext rpy2.ipython

Now we are done. Change the runtime back to R, and it can access files in your google drive following the path "/content/drive/MyDrive/".  As far as I can tell, google drive will stay mounted for a while even when you leave and go back to google colab. In case the connection is lost, just run it again. 

For your convenience, I shared a notebook file that contains the above codes, Click on the link below, it should automatically show up in your google colab. 

mountdrive.ipynb





Comments

Post a Comment

Popular posts from this blog

Syllabus

Image
   qsbrii2025.blogspot.com Policy on video recording or remote access 1. All lectures are in-person. Students are strongly encouraged to attend, especially for R-sessions.  2. The video recordings of the lectures will NOT be available for any personal or professional reasons. However, all lecture notes and homework are available online, and the students are encouraged to schedule (remote or in-person) office hours with me.  3. Remote access by zoom will be available. However, all attendees will be muted but you can communicate through chat . I expect that you will join zoom from a private and quiet environment.  Canvas vs blogspot.com 1. ALL lecture notes, homework assignments, and other teaching material are only available on qsbrii2025.blogspot.com. 2. Canvas will be used for class announcement ONLY.   Time and Location  MW 1:20-2:40 F 1:20-3:00 Foch 3rd floor Lecture Hall  or ED Center lower floor (10/1, 10/17) GOAL:  Build ...
Read more

Lecture 3

Lecture 3, Oct 3, 2025 Slides Jupyter Notebook The dataset I used in the Lecture can be downloaded  here .  HW 3 (Due Oct 10, Friday).  1 .  A SNP locus is genotyped for a total of 1000 individuals, among which 485 is AA, 421 is Aa, and 94 is aa. Compute the $X^2$  statistic for Hardy-Weinberg Equilibrium, and find the P-val. You can either use function  pchisq  or use your simulated reference distribution. 2. Genetic Association Test Genetic Association studies have been very popular in last two decades. Billions of dollars have been spent and tens of millions individuals have their genomes genotyped. They all look for a simple signal. That is, the distribution of genotypes differ among people with different phenotypes. Consider a study with diabetes. Say we recruited 1000 diabetes patients, and 1500 controls. Assume that they are from the same genetic background, which is very important. If the patients are recruited in US, and co...
Read more

Lecture 2 + Lab

Slides  Jupyter Notebook  for the lab.  Jupyter Notebook  for detailed notes, R code and results Homework 2 1. Finish Task 4 of the Lab. Show your code and results. 2 . Do a numerical experiment to generate the sampling distribution of $X^2$  statistics for HWE (the more realistic one with estimated allele frequency), but choose different allele frequencies and sample sizes, to determine if the sampling distribution is approximately  $X^2$  regardless of the underlying allele frequencies.
Read more