How to use the goseq for ensemble gene ID

Question

[BISEP]

Hello I am working on mouse RNA seq data, now I have list of genes which are of ensemble gene IDs I wanted to perform gene ontology using goseq. Can anyone help me with the example code which will be Very helpful do proceed with my analysis

I tried but not able understand what to do

what I have tried

library(goseq) library(GenomicFeatures) library(TxDb.Mmusculus.UCSC.mm10.ensGene)

gene=read.table("data", header=T)

gene=gene$geneID

tx <- transcriptsBy(TxDb.Mmusculus.UCSC.mm10.ensGene)

length <- median(width(tx))

length=length[gene]

pwf=nullp(gene,bias.data=length)

[jared.andrews07]

What have you tried and what errors have you encountered? Biostars is not a code writing service, though people are usually willing to help you fix what might be going wrong in your code if you post it.

[BISEP]

@jared.andrews07 thank you for the response sorry, I have edited my question given some code can you suggest me how can I resolve my issue, data file containes the only ensembl gene ids

Thank you

[ATpoint]

Is this the same as here?

https://support.bioconductor.org/p/9135955/

[ATpoint]

If this is just some arbitrary genes that do not come from a DEG analysis do you really need goseq and its "bias" nullp function? Why not simply load the genes into a webbased solution such as gprofiler2 or EnrichR?

[BISEP]

@ATpoint Thank you