How to use the goseq for ensemble gene ID
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)
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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.
@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
Is this the same as here?
https://support.bioconductor.org/p/9135955/
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?
@ATpoint Thank you