A chord plot for miRNA IDs by GOplot package

Question

[Morteza Hadizadeh]

Dear all,

I hope all of you be fine and healthy.

I want to create a chord plot by GOplot package. My input data includes miRNA IDs. After performing the subsequent command, I encounter the following error:

chord <- chord_dat(circ, genes, process)
Error in `[<-`(`*tmp*`, g, p, value = ifelse(M[g] %in% sub2$genes, 1,  : 
  subscript out of bounds

I guess the input data must be gene symbols (not miRNA IDs). Is it right?

I would be grateful if you could guide me to resolve it.

[Hamid Ghaedi]

To reproduce the error, could you share a slice of the data and code you used?

Answer 1

[Print My Rugs]

I suspect that you encounter this error because the selection "genes" that you are supplying does not match with the IDs provided in the "circ" object. This could be because of different ID types (Gene name vs Ensembl) or differences in the formatting (Ace vs ACE).