Hello, I am working with the R package WebGestaltR_0.4.4. I have been using
for two years without problems. Today I got the "Organism is missing error" when I use the
WebGestaltR function on the same dataset I used without problems in the past. I tried both the ORA and GSEA analyses, and other hsapiens and mmusculus datasets, but I get always the same error. I suspect that the APIs are not working, as is suggested from the traceback I am posting here. Would it be possible to fix this?
8.
7.
idMappingGene(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile,
inputGene = inputGene, sourceIdType = sourceIdType, targetIdType = targetIdType,
collapseMethod = collapseMethod, mappingOutput = mappingOutput,
outputFileName = outputFileName, hostName = hostName)
6.
idMapping(organism = organism, dataType = dataType, inputGeneFile = inputGeneFile,
inputGene = inputGene, sourceIdType = geneType, targetIdType = NULL,
collapseMethod = collapseMethod, mappingOutput = FALSE, cache = cache,
hostName = hostName)
5.
.uploadGeneExistingOrganism(organism = organism, dataType = dataType,
inputGeneFile = inputGeneFile, inputGene = inputGene, geneType = geneType,
collapseMethod = collapseMethod, geneSet = geneSet, cache = cache,
hostName = hostName)
4.
loadInterestGene(organism = organism, dataType = "rnk", inputGeneFile = interestGeneFile,
inputGene = interestGene, geneType = interestGeneType, collapseMethod = collapseMethod,
cache = cache, hostName = hostName, geneSet = geneSet)
3.
WebGestaltRGsea(organism = organism, enrichDatabase = enrichDatabase,
enrichDatabaseFile = enrichDatabaseFile, enrichDatabaseType = enrichDatabaseType,
enrichDatabaseDescriptionFile = enrichDatabaseDescriptionFile,
interestGeneFile = interestGeneFile, interestGene = interestGene, ...
2.
WebGestaltR(organism = "hsapiens", enrichDatabase = cateGory,
outputDirectory = OUT.DIR.GSEA[[1]], enrichMethod = "GSEA",
interestGene = rankList[0:1000, ], interestGeneType = "ensembl_gene_id",
nThreads = 20, projectName = projName, ...)
1.
gseaEnrich_single(resLFC_D7.anno, "Day7_G203G_G203R", "geneontology_Biological_Process",
sigMethod = "top", topThr = 40)