-
Notifications
You must be signed in to change notification settings - Fork 85
-
Notifications
You must be signed in to change notification settings - Fork 85
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Acute problem: LinkPeaks error #858
Comments
I followed this line by line and problem is same we encountered earlier with GeneActivity function. LinkPeaks() does have this hardcoded: Meaning that gene id given to it must be gene name and not gene id. Our data is Ensembl id based thus this fails. |
Hi @laasov, I've added a parameter to control whether to use gene names or gene IDs in the gene annotations ( Could you try installing from the develop branch and see if setting this parameter solves the issue? |
Hello @timoast. Thank you! Seems like this got rid of the previous error. However, running
now stops with an error:
Traceback:
May I open another issue for this error or would it be okay to study the error under this one? |
Can you show what is |
Sure!
|
Thanks, I think I found the issue. Can you try reinstalling from the develop branch and see if it's fixed? |
Thanks, it got past that point. One more thing, I guess. It prints:
Traceback (if that helps to locate the problem) tells that it comes from Edit: Whoops, forgot to mention this came after reinstalling the package. |
Ah, looks like I missed one. Made some more updates, hopefully it's fixed for real now |
No worries! However, I'm afraid it's still missing something. It prints:
|
Ok should be fixed now |
Looks good, at least Signac::Links returns reasonable-looking values. Thank you so much and congratulations on your new paper! Closing this issue. |
Hi,
LinkPeaks produces an unexpected error when I try to run it:
Error:
Testing 4 genes and 107523 peaks
Error in LinkPeaks(rv2.ss, peak.assay = "peaks", expression.assay = "RNA", :
No peaks fall within distance threshold
Have you set the proper genome and seqlevelsStyle for peaks assay?
Here lp.genes is a vector containing ENSMUS IDs (as are the rownames of RNA assay) for which I know there are expected to be correlated peaks within the distance parameter. Thus, the error shouldn't rise from that. The data object contains data from typical chromosomes, but seqlevels returns also other chr-tags:
I'm using R version 4.1.1 and Signac version 1.4.0. Info on these and other properties can be found from session info below
Thank you!
The text was updated successfully, but these errors were encountered: