R package for GO-BP enrichment analysis with c(symbol, log2foldchange, pvalue)

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3.7 years ago

choijamtsm ▴ 60

Hello everyone.

I am trying to get mmu GO-BP pathways from mRNA deseq2 data from mouse:

Here is input data:

input_genes 
#        Symbol log2FoldChange.case.control.         Padj
#1          Cnn2                    -1.024326 9.830000e-67
#2         Prkg2                    -2.702457 8.240000e-32

As you can see i have gene symbol, log2foldchange, and padj data. Which R package can i use it for mmu GO-BP analysis? I tried topGO but this input data not enough for that.

Is there any alternative R package for mouse GO-BP analysis based on these 3 column?

Thank you so much

RNA-Seq R GO • 879 views

ADD COMMENT • link 3.7 years ago by choijamtsm ▴ 60

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What do you mean by "this input data is not enough" for topGO. As far as I'm aware topGO just requires a list of differentially expressed genes?

Anyway, for GO analysis of RNA-seq data I would always recommend goseq.

ADD REPLY • link 3.7 years ago by i.sudbery 19k

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