Unable to Use targetScan function with mapply

[fischuu]

Unable to Use targetScan function with mapply

[fischuu]

Hi,
targetScan() returns actually a matrix with 4 columns and maxOut rows (i.e. in your case a 5x4 matrix) for each miRNA. However, mapply tries to simplify the output by default, meaning it tries to create a single matrix and/or vector for all the joint calls.

Of course, in your case this is not possible and you would like to keep the list of matrices (=each list item represents the output matrix per miRNA), so you need to set SIMPLIFY=FALSE (this option is really capitalised...).

So, the complete command that should do what you want is

test <- mapply(targetScan, mirna=c("hsa-miR-99b-5p", "hsa-miR-99b-3p", "hsa-miR-99a-5p"),
               species = "Human", 
               release = "7.2", 
               maxOut = 5, 
               SIMPLIFY=FALSE)

Here, you can also rely on the recycling of vectors in R, so the input for species, release and maxOut does not need to be repeated. I hope this helps, in case you need more help, please let me know.

I took this issue also as motivation to rewrite the function such that it accepts vectors as input in mirna to avoid this problem in the future.

Now, with the latest package version here in the main branch those both calls work:

targetScan(mirna="hsa-miR-99a-5p", species = "Human", release = "7.2", maxOut = 5)

and

targetScan(mirna=c("hsa-miR-99b-5p", "hsa-miR-99b-3p", "hsa-miR-99a-5p"), 
           species = "Human", 
           release = "7.2",
           maxOut = 5)

[compbiolover]

Thanks @fischuu!
I just installed the new version and it works perfectly. Thanks for clarifying the point about mapply. I am still getting use to thinking about problems in R terms.