Errors related to calculateBsBackground about bindingsitefinder HOT 4 CLOSED

Hi,
thanks for pointing out the error. I'll be looking into it and let you know what we found as soon as possible.

from bindingsitefinder.

I looked into your error and I can't reproduce the error.

I've tested the example from the help that you've posted with your R version (4.3.2) and it works just fine.

Could you please try to setup a clean version of your environment and try to run the example again. If that does not help, then make sure that you have only packages relevant for BindingSiteFinder installed. This helps to further isolate the error.

from bindingsitefinder.

Hi, I found why the error happened during calculateBsBackground.
It was a problem on my gns (gene annotation) object.

This was the function I used for making a gene annotation object.
`create_gns_object <- function(file) {
annoDb = GenomicFeatures::makeTxDbFromGFF(file = file, format = "gtf")
annoInfo = rtracklayer::import(file, format = "gtf")
gns = genes(annoDb)
idx = match(gns$gene_id, annoInfo$gene_id)
elementMetadata(gns) = cbind(elementMetadata(gns),
elementMetadata(annoInfo)[idx,])

gns
}`

Since my annotation file was a gtf format, I used a similar code but imported with format = gtf
Then, I had two columns of gene_id, leading to an error in the downstream functions such as calculateBsBackground.

I fixed the problem with erasing one of the gene_id column.
Then, the code worked perfectly fine after I fixed my annotation object.

Thanks for your help!

from bindingsitefinder.

Perfect thanks for reporting this. We should include a specific error message for duplication of the gene_id column!

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