Obtaining the number of links between Peaks and Genes

[sylestiel]

Is there a way of determining the number of peak2gene links for each gene that meet the cutoffs?

[rcorces]

This information should be available from the return of getPeak2GeneLinks() when returnLoops = FALSE via the idxRNA column. This is explained briefly in this section of the manual:
https://www.archrproject.com/bookdown/peak2genelinkage-with-archr.html

[sylestiel]

Can you elaborate some more. I tried writing the peakset and geneset files under peak2gene links to csv but although I see the gene names with IRanges in the later and GRanges in the former I still don't understand how to associate the actual number of Links associated with a given gene(s).

[sylestiel]

If idx is the index for each message then the only way of arriving at the number of links seems rather laborious and manually. If there is a simpler way of doing so do advice.

[rcorces]

From the manual:
"the indexes for the scRNA-seq gene are stored in the idxRNA column"
so idxRNA is a numeric index of the gene from your RNA data. so if you count the number of observations of each idxRNA and map them back to the gene symbol, you get what you are looking for.

[sylestiel]

Thanks a bunch! Already on it. Hence the manual part.