ERROR: dependencies ‘clue’, ‘Cairo’, ‘doParallel’ are not available for package ‘ComplexHeatmap’

[jielab]

Hi, guys:

I got the following error. I am using Windows 11 WSL, Ubuntu Linux.

Can you please let me know how to resolve this?

Thank you very much & best regards, Jie

[cuelee]

Hi Jie,

Sorry for the inconvenience. We tested PLEIO on the Mac OS and the Linux environments, but we haven't tested it on the Windows OS environment yet. The error message tells you that R does not have all dependencies required before installing the package.

A possible alternation is to install the necessary dependencies manually by putting the following commands in R: install.packages(“clue”) install.packages(“Cairo”) install.packages(“doParallel”)

Then, install ComplexHeatmap by: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("ComplexHeatmap")

Let me know if you have any further questions.

Thanks, Cue Hyunkyu Lee

[jielab]

Dear Cue:

Thank you very much! It now works!

I am able to run the example and generate the nice looking circular plot.

My question is: how could we analyze and plot pleiotropy based on a single SNP?

Best regards, Jie

[cuelee]

It seems I didn't understand the question correctly. Could you please elaborate on the question for me?

Best Regards, Cue Hyunkyu Lee

[jielab]

Dear Cue:

I wrote something about pleiotropy 10 years ago, being the first author of the following two papers:

1. Jie Huang, et al. 2010. Cross-Disorder Genomewide Analysis of Schizophrenia, Bipolar Disorder, and Depression
2. Jie Huang, et al. 2011. PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies.

I did not work much on this field over the past 10 years. A lot of methods and tools seem to have developed. The concept of pleiotropy even changed. Now there is "horizontal pleiotropy" and "vertical pleiotropy". Now "cross-disorder" become "colocalization" and it crosses from GWAS to eQTL...

I followed the tutorial of your Github. At the end, it says: This command will generate rs12073392.jpeg at the input_directory. To generate a pleiotropy plot for SNPs other than rs12073392, you can add RSIDs in snp.txt.gz. This rs12073392.jpeg picture looks very nice. My question is: is the pleiotropy analysis based on this single SNP rs12073392?

Don't kow if you are still actively maintaining PLEIO. If I could get in touch with you, can you pease reply to my email jiehuang001@gmail.com?

Best regards, Jie

[cuelee]

Dear Jie,

Thank you very much for the detailed description.

Updates on PLEIO Github have been being delayed. I recently started my postdoc, and I have limited time to update the page. I will update the information as soon as I settle into a new environment. (in a month approximately)

A brief background information

In my research(PLEIO), pleiotropy refers to the phenomenon where a locus affects multiple traits. PLEIO, a python code, can analyze summary statistics from multiple traits to identify pleiotropic loci. The loci identified by PLEIO show a pleiotropic association pattern, and the pleiotropyPlot, an R code, is a tool that visualizes these pleiotropic association patterns. Please see my publication for more details.

Answer to your question

pleiotropyPlot uses analysis results of PLEIO analysis. You can visualize any number of SNPs. In the provided example in the Github page, I visualized the pleiotropic association pattern of a single SNP 'rs12073392'.

If you need my help, please feel free to contact me. If so, let me know the details of your current research and the goal of your analysis. You can send me an email at: hl3565@cumc.columbia.edu

Sincerely, Cue Hyunkyu Lee