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bzhanglab / WebGestaltR

R package for WebGestalt
https://bzhanglab.github.io/WebGestaltR/
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How can kinase targets be predicted by WebGestaltR function #11

Open QifengOu opened 3 years ago

QifengOu commented 3 years ago

just like to perform the enrichment analysis, How can kinase targets be predicted by WebGestaltR function. for example:

rankFile <- system.file("extdata", "GeneRankList.rnk", package="WebGestaltR") outputDirectory <- getwd() enrichResult <- WebGestaltR(enrichMethod="GSEA", organism="hsapiens", enrichDatabase="pathway_KEGG", interestGeneFile=rankFile, interestGeneType="genesymbol", sigMethod="top", topThr=10, minNum=5, outputDirectory=outputDirectory)

We change the parameters enrichDatabase="pathway_KEGG" to enrichDatabase='kinases_target'.

Also, can you provide a detailed code example? Think you very much!!

QifengOu commented 3 years ago

I want to download the GMT file used by the website tool. Could you please provide the download link or gmt file