Off topic:Enrichpathway In ReactomePA.
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6.0 years ago
bikash2510 ▴ 30

When I am trying to do enrichpathway in ReactomePA package, I am getting zero observation. No entrezid is mapped.

> gene<-c("64240", "6296", "196883", "153", "155", "4299", "2334", "79026", 
    "9495", "1109", "23294", "50636", "343", "394", "50649", "23204", 
      "728619", "440", "23300", "90135", "695", "399947", "84645", 
     "401027", "401097", "727", "767", "57685", "23473", "858", "126075", 
        "6348", "6351", "901", "729230", "952", "1013", "54825", "10715", 
         "79094", "337876", "163732", "51192", "22866", "256076", "594855", 
         "1373", "1395", "122011", "8048", "8530", "441521", "115908", 
         "1511", "340578", "8526", "729582", "1742", "58512", "28514", 
         "1756", "26052", "1791", "100130771", "93556", "8672", "954", 
         "2034", "83715", "83648", "400823", "2274", "23768", "114984", 
        "118924", "9846", "2650", "219970", "653641", "2974", "51454", 
        "3040", "54435", "55363", "3091", "9454", "59340", "51214", "3554", 
        "3653", "122953", "386679", "54900", "116842", "3963", "3981", 
         "22998", "114038", "158038", "80350", "84918", "10150", "79150", 
         "440823", "4312", "4352", "56667", "83955", "79923", "89796", 
         "606", "9611", "64067", "4883", "56675", "9378", "4914", "126014", 
         "165140", "10039", "23037", "221692", "51588", "118788", "10769", 
         "51090", "23129", "5435", "285755", "5504", "29968", "11168", 
         "5733", "5746", "22931", "378948", "51308", "5979", "57127", 
         "56163", "649946", "6278", "6286", "148418", "6403", "710", "5274", 
         "26040", "81537", "83699", "148641", "85414", "159963", "6536", 
         "23657", "55512", "6619", "100126781", "84973", "26770", "728524", 
        "6689", "6696", "6704", "6708", "6767", "90627", "6779", "474338", 
         "100130958", "85360", "1155", "122402", "7006", "100124696", 
         "7015", "7019", "53346", "284186", "160418", "8794", "7293", 
         "7170", "7173", "373", "7222", "1831", "7291", "7302", "10537", 
         "10720", "80329", "7402", "7422", "79674", "7453", "9589", "54739")

>> yy = enrichPathway(gene, pvalueCutoff=0.05)

>>head(yy)

[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust    qvalue      geneID     
[9] Count      
<0 rows> (or 0-length row.names)
R ReactomePA • 2.4k views
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