miRNAtap getPredictedTargets error message
Entering edit mode
Assa Yeroslaviz ★ 1.5k
Last seen 4 days ago
Munich, Germany

Hi Maciej,

I have found your package in the bioconductor repository, when I started working on miRNA. I have a data set from mouse for which I have identified significantly deregulated miRNA using miRDeep2.

Now I try to predict the targets of these miRNAs. For that I wanted to use you package.
Unfortunately it doesn't exactly do what i would like it to do.

these are my commands:

mir <- list("let-7a", "mmu-miR-17-5p", "mmu-miR-6238")
predictions = lapply(X = mir,FUN =  getPredictedTargets, method ='geom')

For that query I get the following error message:

Error in `[.data.frame`(ranks, , 2:(n_valid_srcs + 1)) :
  undefined columns selected
In addition: Warning message:
In FUN(X[[i]], ...) :
  sources which returned a target list<min_src, min_src reduced to -1

I think I know the source of the error. This is because the miRNA "mmu-miR-6238" is probably not in the data base of any of the sources you use in your package.

I was wondering if it is possible to add/modify the package, so that it will give a warning and not an error when executing it with miRNAs which are not in the data base.
That said I was wondering if there is a better option of calling the getPredictedTargets command on multiple miRNAs other than creating a list and getting back a list structure.

thanks in advance



miRNAtap miRNA target prediction • 578 views
Entering edit mode
Maciej • 0
Last seen 5.6 years ago
United Kingdom

Thanks for reporting it Assa!

You were right, somehow I must have missed one case, fixed it now, it returns NULL and shows a warning to the used. Pushed the update to devel, if everything works ok I'll push to production tomorrow so you will be able to update it and use it shortly.

Let me know if you spot anything else.


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