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ldg21 / SGSeq

Splice event prediction and quantification from RNA-seq data
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The output with the annotated splice variants #4

Open OlgaVT opened 4 years ago

OlgaVT commented 4 years ago

Hi, I was trying to figure out how to get the nice output with the splice variants in terms of "SE", "AFE" and so on. Now I am using mcols(), but are there better ways? Thank you!

ldg21 commented 4 years ago

Hi,

Thanks for your interest in SGSeq.

annotateSGVariants() is a low-level function used by findSGVariants() and not currently exported to the namespace (i.e. not visible to the user). SGVariants are complicated objects, so it is recommended to the create them with findSGVariants(). However if you do need to call the annotation function directly you can do so with SGSeq:::annotateSGVariants.

If you have more questions please consider posting to the bioconductor support website.

Leonard

On Sat, Apr 4, 2020 at 5:30 AM OlgaVT notifications@github.com wrote:

Hi,

I wonder, if there is a way to get the annotation of events in terms of "exon skipping", "intron retention" and so on. I've found the reference of the function "annotateSGVariants". This command: ?annotateSGVariants gives me the manual, but this: annotateSGVariants():

Error in annotateSGVariants() : could not find function "annotateSGVariants"

Also, this function is only mentioned in the reference manual, but not described. Does it exist or are there any alternatives?

Thank you!

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OlgaVT commented 4 years ago

Hi, thank you for the answer. I had some misunderstanding about this function, now it is clear.