Error in startsWith(gmtFile, "http://") : non-character object(s)

[ilian atanassov]

Hello,

I am getting the following error:

Error in startsWith(gmtFile, "http://") : non-character object(s)

When running the following code:

quant_data_long %>%
        filter(!is.na(`Gene name`)) %>%
        filter(comparison == "D1 / D0") %>%
        select(`Gene name`, logFC) %>%
        as.data.frame() %>%
        WebGestaltR(enrichMethod = "GSEA",
                    organism = "mmusculus",
                    hostName="https://www.webgestalt.org/",
                    enrichDatabase = "geneontology_Biological_Process_noRedundant",
                    enrichDatabaseType = "genesymbol",
                    collapseMethod = "mean",
                    saveRawGseaResult = TRUE,
                    projectName = "D1_vs_D0")

Does this have to do with the ID mapping? Do I need to map gene symbols to Entres IDs prior to running the GSEA enrichment?

Best wishes,

Ilian

[ilian atanassov]

Hello,

The error was coming from the way that I was providing the parameters for WebGestaltR. The following code doesn't throw this error:

quant_data_long %>%
        filter(!is.na(`Gene name`)) %>%
        filter(comparison == "D1 / D0") %>%
        select(`Gene name`, logFC) %>%

        write_tsv("D1_vs_D0.rnk", col_names = FALSE)

       
WebGestaltR(enrichMethod = "GSEA",
                    organism = "mmusculus",
                    hostName="https://www.webgestalt.org/",

                    enrichDatabase = "pathway_KEGG",
                    interestGeneFile = "D1_vs_D0.rnk",
                    interestGeneType="genesymbol",

                    collapseMethod = "mean",
                    saveRawGseaResult = TRUE,
                    projectName = "D1_vs_D0")

Best wishes,

Ilian

[Yuxing Liao]

Hi,

It is probably because you mean interestGeneType="genesymbol" instead of enrichDatabaseType = "genesymbol". enrichDatabaseType is for user provided GMT file.

Yuxing

--
You received this message because you are subscribed to the Google Groups "webgestalt" group.
To unsubscribe from this group and stop receiving emails from it, send an email to webgestalt+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/webgestalt/e9913d1e-6e16-4be6-8502-c487d27b19ean%40googlegroups.com.