In xtfrm.data.frame(x) : cannot xtfrm data frames

[ldutoit]

Hi,

thanks for such an easy and useful piece of software!

When I run radsex_map_circos or radsex_map_manhattan

I get the error:

In xtfrm.data.frame(x) : cannot xtfrm data frames

It happens in R 4.1.0 and 4.3.1 with the attached sample dataset.

These people : https://community.rstudio.com/t/error-in-xtfrm-data-frame-x-cannot-xtfrm-data-frames/171618

Say it can be solved by changing tibble to data frame, and I believe the problem in the function load_genome_metrics()

But I am not quite sure how to solve it from there, any help would be greatly appreciated.

Kind regards

Ludo alignment_results2.tsv.zip

[biodray]

Hi,

I encountered the same problem, and it looks like it's the ordering process in the function load_genome_metrics() that is not working:

unplaced_lengths <- unplaced_lengths[order(unplaced_order, decreasing = TRUE),]

The function order is not working anymore on a dataframe, only on a vector. I think this should work:

unplaced_lengths <- unplaced_lengths[order(unplaced_order[,1], decreasing = TRUE),]

[ldutoit]

Hi audrey,

that is amazing, thanks for helping. I re-defined the function after modifying this function but I still have the same problem.

I am not exactly sure where the bug is, there are a lot of order functions in load_genome_metrics.

Ludo

[ldutoit]

Hi Audrey,

Thanks for that! I have not been able to test it yet, but people I don't know helping with one of my problems is a real big highlight of my week.

Thank you

Ludo

On Thu, 16 Nov 2023 at 07:50, Audrey Bourret @.***> wrote:

Hi,

I encountered the same problem, and it looks like it's the ordering process in the function load_genome_metrics() that is not working:

unplaced_lengths <- unplaced_lengths[order(unplaced_order, decreasing = TRUE),]

The function order is not working anymore on a dataframe, only on a vector. I think this should work:

unplaced_lengths <- unplaced_lengths[order(unplaced_order[,1], decreasing = TRUE),]

— Reply to this email directly, view it on GitHub https://github.com/SexGenomicsToolkit/sgtr/issues/4#issuecomment-1813082121, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBMMAJ3M4SOVYNKWX2CEXDYEUFHFAVCNFSM6AAAAAA67CSJOCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJTGA4DEMJSGE . You are receiving this because you authored the thread.Message ID: @.***>

[zhanghong9869]

Hi, I'm having the same problem as you. ![Uploading 屏幕截图 2024-04-17 162303.png…]()

[zhanghong9869]

May I ask how you solved it?

[biodray]

Hi @zhanghong9869, I modified a function within the packages, but since my pull request of this modification is not yet accept in the main package, you can install directly my modified version of sgtr like this:

library(devtools) install_github("biodray/sgtr") library(sgtr)

You can find the exact modifications in my package copy here: https://github.com/biodray/sgtr Or in my pull request here: https://github.com/SexGenomicsToolkit/sgtr/pull/5

[zhanghong9869]

Hi @Audrey Bourret, I followed the method you provided and the issue has been resolved. Thank you very much, my partner from Canada. You're a great person!

[carolhsb]

Hi I am having the same problem as well :S @biodray I tried your modified version and it didn´t work I am trying to use the plot_manhattan function