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ldg21 / SGSeq

Splice event prediction and quantification from RNA-seq data
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Error from predictVariantEffects function #7

Open smartgamer opened 3 years ago

smartgamer commented 3 years ago

Hi,

I got this error from predictVariantEffects function:

vep <- predictVariantEffects(sgvc_pred, txdb, Hsapiens) [updateObject] Validating the updated object ... OK [updateObject] Validating the updated object ... OK Error in validObject(.Object) : invalid class “SGFeatures” object: invalid object for slot "featureID" in class "SGFeatures": got class "numeric", should be or extend class "integer" In addition: Warning messages: 1: In .set_group_names(grl, use.names, txdb, by) : some group names are NAs or duplicated 2: In .set_group_names(grl, use.names, txdb, by) : some group names are NAs or duplicated 3: In max(featureID(features)) : no non-missing arguments to max; returning -Inf

Do you have any solution to this?

ABU-TO commented 2 years ago

I got the same error "Error in validObject(.Object): invalid class “SGFeatures” object: invalid object for slot "featureID" in class "SGFeatures": got class "numeric", should be or extend class "integer"" for me, I find the sgvc_pred is empty, maybe check the “SGFeatures” object helps.

For the more. my code is: '''' library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(BSgenome.Hsapiens.UCSC.hg38) seqlevelsStyle(Hsapiens) <- "UCSC" vep <- predictVariantEffects(sgvc_pred,TxDb.Hsapiens.UCSC.hg38.knownGene, Hsapiens) vep ''''

gabriella-quinn commented 8 months ago

I am having the same issue, sadly 2 years later.