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