yxngl
commented
2 years ago Hi, geneFile <- system.file("extdata", "interestingGenes.txt", package="WebGestaltR") get example data from the package. The files are in gene symbols. You should just use the file path to your input files.
On Sat, May 28, 2022 at 4:38 PM integratebio @.***> wrote:
Hello, I am using the WebGestaltRs 0.4.4 version on R 4.1.2. I got the ERROR: No IDs are mapped error when I provided Ensembl gene ids using interestGeneType="ensembl_gene_id" and referenceGeneType="ensembl_gene_id" arguments to the example code from the vignette i.e.
geneFile <- system.file("extdata", "interestingGenes.txt", package="WebGestaltR") refFile <- system.file("extdata", "referenceGenes.txt", package="WebGestaltR") outputDirectory <- getwd() enrichResult <- WebGestaltR(enrichMethod="ORA", organism="hsapiens", enrichDatabase="pathway_KEGG", interestGeneFile=geneFile, interestGeneType="ensembl_gene_id", referenceGeneFile=refFile, referenceGeneType="ensembl_gene_id", isOutput=TRUE, outputDirectory=outputDirectory, projectName=NULL)
The full error message was as follows:
Loading the functional categories... Loading the ID list... ERROR: No IDs are mapped. Please check your input.Error in idMappingGene(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile, : ERROR: No IDs are mapped. Please check your input.
For your reference, here are the input files I used: interestingGenes.txt https://github.com/bzhanglab/WebGestaltR/files/8791891/interestingGenes.txt referenceGenes.txt https://github.com/bzhanglab/WebGestaltR/files/8791890/referenceGenes.txt (protein coding genes) They are indeed Ensembl IDs. So I am not sure why I am getting this error.
Could you please let me know you advice on how I should be providing the Ensembl gene ids as input?
PS: I should note that interestingly, if I provide the same inputs i.e. Ensembl IDs with interestGeneType="genesymbol" and referenceGeneType="genesymbol" arguments, I don't get the error. But I am not sure if should trust the outputs of the enrichment analysis I got by this way. I would like if I could explicitly "tell" WebGestaltR that I am providing Ensembl IDs. I hope there is a way to do that.
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Hello, I am using the
WebGestaltRs 0.4.4 version on R 4.1.2. I got theERROR: No IDs are mappederror when I provided Ensembl gene ids usinginterestGeneType="ensembl_gene_id"andreferenceGeneType="ensembl_gene_id"arguments to the example code from the vignette i.e.The full error message was as follows:
For your reference, here are the input files I used: interestingGenes.txt referenceGenes.txt (protein coding genes) They are indeed Ensembl IDs. So I am not sure why I am getting this error.
Could you please let me know you advice on how I should be providing the Ensembl gene ids as input?
PS: I should note that interestingly, if I provide the same inputs i.e. Ensembl IDs with
interestGeneType="genesymbol"andreferenceGeneType="genesymbol"arguments, I don't get the error. But I am not sure if should trust the outputs of the enrichment analysis I got by this way. I would like if I could explicitly "tell"WebGestaltRthat I am providing Ensembl IDs. I hope there is a way to do that.