ERROR: dependencies 'Gviz', 'biomaRt' are not available for package 'eQTpLot'

[jielab]

Hi, there:

I trired to install, but got the following errors. It seems that a lot of dependency packages are not available for R 4.1.1.

ERROR: dependencies 'Gviz', 'biomaRt' are not available for package 'eQTpLot'

• removing 'D:/software_win/R_lib/eQTpLot' Warning messages: 1: packages ‘snpStats’, ‘biomaRt’, ‘Gviz’ are not available for this version of R Versions of these packages for your version of R might be available elsewhere,

Can you please kindly provide an easy solution so that I could get this installed?

Thank you very much & best regards, Jie

[anastasia-lucas]

Hi Jie,

Thanks for using our package.

Can you try installing those packages first using BiocManager?

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Gviz") BiocManager::install("biomaRt") BiocManager::install("snpStats")

Then try installing eQTpLot again using devtools::install_github("RitchieLab/eQTpLot")

[jielab]

Dear Anastasia:

Thanks!

Please see the screenshot below. Now there is a new message. It still does not work.

Best regards, Jie

[anastasia-lucas]

Hi Jie,

Are you able to install other packages from GitHub using devtools::install()?

If you need a lightweight test with no dependencies, you could try devtools::install_github("anastasia-lucas/sqlizeR") or any other R package.

Unfortunately install.packages() method won't work as this is not on CRAN.

[jielab]

Dear Anastasia:

I tried it again and this time it worked. Please see attached.

There days there are many many tools about colocalization analysis. So, eQTpLot is mainly for "plot" after the colocalization analysis was done? Is there a pipelien for conducting colocalization analysis at genome-wide level?

Don't know if you are aware of LocusFocus, which claims to do the colocalization analysis through an easy web interface. I tried it too, but it did not work yet.

Best regards, Jie

[anastasia-lucas]

Hi Jie,

Yes, you are correct that eQTpLot is focused on the visualization.

I am not aware of any existing pipeline, but I know that a few people in my group are working on making a pipeline available for conducting colocalization between GWAS trait and eQTL.