yxngl
commented
1 year ago Sorry. I have been busy with a manuscript recently and just replied in the Google Forum.
On Wed, Jul 27, 2022 at 12:42 PM nhu119 @.***> wrote:
Thank you for developing and maintaining WebGestalt. I have been using the R package to perform Over-Representation Analysis and would like to use the latest GO gene sets from MSigDB (v7.5.1; http://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/7.5.1/c5.go.v7.5.1.symbols.gmt). I used the function "readGmt" to lead the .gmt file into my R environment, and then I tried running the WebGestaltR function using the following command
WebGestaltR(enrichMethod="ORA", organism="hsapiens", enrichDatabaseFile = Go, enrichDatabaseType = "genesymbol", interestGene=sig_genes, interestGeneType="genesymbol", referenceSet="genome_protein-coding", referenceGeneType="genesymbol", minNum=5, sigMethod="top", topThr=20, isOutput=TRUE, outputDirectory=outputDirectory, projectName=outName)
When I run it, I get the following error:
"Error in startsWith(gmtFile, "http://") : non-character object(s)"
I double checked my .gmt fie, and all columns are characters. Can you please offer some insight as to why I am getting this error? As an aside, I have been able to successfully run WebGestaltR using the gene set files readily available with the package using "enrichDatabase". Thank you so much for your time, help, and insight.
— Reply to this email directly, view it on GitHub https://github.com/bzhanglab/WebGestaltR/issues/16, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAM6IVOXSR5FR5C2GFOSRQ3VWFYIXANCNFSM542N347A . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Thank you for developing and maintaining WebGestalt. I have been using the R package to perform Over-Representation Analysis and would like to use the latest GO gene sets from MSigDB (v7.5.1; http://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/7.5.1/c5.go.v7.5.1.symbols.gmt). I used the function "readGmt" to lead the .gmt file into my R environment, and then I tried running the WebGestaltR function using the following command
WebGestaltR(enrichMethod="ORA", organism="hsapiens", enrichDatabaseFile = Go, enrichDatabaseType = "genesymbol", interestGene=sig_genes, interestGeneType="genesymbol", referenceSet="genome_protein-coding", referenceGeneType="genesymbol", minNum=5, sigMethod="top", topThr=20, isOutput=TRUE, outputDirectory=outputDirectory, projectName=outName)
When I run it, I get the following error:
"Error in startsWith(gmtFile, "http://") : non-character object(s)"
I double checked my .gmt fie, and all columns are characters. Can you please offer some insight as to why I am getting this error? As an aside, I have been able to successfully run WebGestaltR using the gene set files readily available with the package using "enrichDatabase". Thank you so much for your time, help, and insight.