使用GOplot包中的circle_dat函数时出错

时间:2018-01-24 18:15:17

标签: r list sum

任何人都有使用GOplot的经验,请帮助我处理此错误?感谢

我正在创建数据以按GOplot绘制图表,但它与

错误
circ <- circle_dat()
  

总和(值)错误:无效&#39;输入&#39;参数(列表)

如下:

category <- rep("BP",8)

ID <- c("GO:0016032","GO:0043207","GO:0045087","GO:0002252","GO:0051607","GO:0034097","GO:0050792","GO:0045088")

Term <- c("Viral process","Response to external biotic stimulus","Innate immune response","Immune effector process","Defense response to virus","Response to cytokine","Regulation of viral process","Regulation of innate immune response")

Genes <- c("BATF2, NMI, BST2, CXCL9, TRIM14, RSAD2, OAS2, STAT1, CCL5, S100A14, TRIM21, CXCL10, DDX58, OASL, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58","NMI, CXCL9, TRIM14, RSAD2, OAS2, STAT1, CCL5, S100A14, TRIM21, CXCL10, DDX58, OASL, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58","BST2, CXCL9, TRIM14, RSAD2, OAS2, CCL5, FURIN, TRIM21, CXCL10, DDX58, IFIT1, OASL, ISG15, MB21D1, MX2, DHX58 ","BATF2, BST2, CXCL9, RSAD2, OAS2, CCL5, S100A14, CMPK2, CXCL10, DDX58, OASL, IFIT1, ISG15, MB21D1, MX2, DHX58","NMI, TRIM14, RSAD2, STAT1, CCL5, S100A14, TRIM21, DDX58, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58","DDX58, OASL, IFIT1, BST2, ISG15, MB21D1, IRF7, CXCL9, RSAD2, OAS2, MX2, DHX58, CXCL10","DDX58, OASL, IFIT1, BST2, ISG15, MB21D1, CXCL9, RSAD2, OAS2, MX2, DHX58, CXCL10","IFIT1, NMI, PARP9, ISG15, IRF7, CXCL9, CCL5, STAT1, MX2, TRIM21, CXCL10")

q.val <- c(0.000000018,0.000000969,0.000000074,0.000146408,0.000000476,0.003476769,0.000063716,0.001187458)

psc1 <- vector()

psc1$david <- data.frame(category,ID,Term,Genes,q.val)
  

警告讯息:   在psc1 $ david&lt; - data.frame(category,ID,Term,Genes,q.val)中:     将LHS强制列入名单

head(psc1$david)
  category         ID                                 Term
1       BP GO:0016032                        Viral process
2       BP GO:0043207 Response to external biotic stimulus
3       BP GO:0045087               Innate immune response
4       BP GO:0002252            Immune effector process\n
5       BP GO:0051607            Defense response to virus
6       BP GO:0034097                 Response to cytokine




    Genes
1 BATF2, NMI, BST2, CXCL9, TRIM14, RSAD2, OAS2, STAT1, CCL5, S100A14, TRIM21, CXCL10, DDX58, OASL, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58\n
2              NMI, CXCL9, TRIM14, RSAD2, OAS2, STAT1, CCL5, S100A14, TRIM21, CXCL10, DDX58, OASL, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58\n
3                                   BST2, CXCL9, TRIM14, RSAD2, OAS2, CCL5, FURIN, TRIM21, CXCL10, DDX58, IFIT1, OASL, ISG15, MB21D1, MX2, DHX58\n
4                                   BATF2, BST2, CXCL9, RSAD2, OAS2, CCL5, S100A14, CMPK2, CXCL10, DDX58, OASL, IFIT1, ISG15, MB21D1, MX2, DHX58\n
5                                         NMI, TRIM14, RSAD2, STAT1, CCL5, S100A14, TRIM21, DDX58, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58\n
6                                                          DDX58, OASL, IFIT1, BST2, ISG15, MB21D1, IRF7, CXCL9, RSAD2, OAS2, MX2, DHX58, CXCL10\n
        q.val
1 0.000000018
2 0.000000969
3 0.000000074
4 0.000146408
5 0.000000476
6 0.003476769

ID <- c ("UBE2L6","IFIT1","S100A14","IFIT5","RSAD2","ISG15","PSMB9","EPSTI1","PARP14","TRIM14","OASL","IFIH1","ST6GALNAC5","ZNFX1","GM2A","OAS2","ARHGAP10","CMPK2","MX2","DDX60","TAP1","PLAC8","PLEKHA7","NMI","CXCL10","MFSD14B","ETV7","IFI6","BATF2","HLADRA","IRF7","FUNDC1","MB21D1","VPS33B","IFI35","ZDHHC2","SDF4","ARFGAP3","AMOTL1","BST2","CXCL9","KIAA1210","STAT1","PARP9","SCAF11","TRIM21","PSMB8","CCT3","PSME1","LOXL3","EXOSC7","CNP","MFSD12","CCL5","NTS","DDX58","PTBP2","DDX27","DHX58","TOR3A","UNC93B1","MAPKAP1","REEP3","USP18","CRYM","FURIN","DOPEY1","SLC25A28","MGMT")

log2FC <- c(4.91216635,6.655472541,2.375439308,4.209728132,1.722467111,2.049068815,6.490325281,6.822595279,3.923398782,4.732497846,4.575484123,1.705875531,4.923436622,2.60827345,1.76254314,2.735952574,4.008416801,5.258289598,4.044999594,4.736550072,6.172050919,4.282501104,3.208171961,5.033929358,2.399759833,2.050897793,2.790055166,2.013796663,3.096102122,3.652784775,2.967372103,2.228560443,4.116356385,1.933960075,1.794503482,2.271099156,1.759847056,2.185965858,5.620065046,4.060212365,2.260535128,5.199032677,2.039404187,1.594577613,3.590903986,1.695054047,1.661676721,1.800940501,3.198116164,6.019076336,1.544051107,3.604409672,2.027346375,5.798190515,2.577687459,5.508644045,1.524049617,3.069782335,1.588483574,1.610455719,2.708812209,1.585058938,1.958513089,6.07876434,2.552673706,2.330685661,1.751220982,1.657774036,1.803929801)
q.val <-c(0.00062886,0.001743489,0.001946228,0.002447293,0.0027105,0.003306247,0.003306247,0.003306247,0.003307595,0.004652201,0.00517898,0.00517898,0.005507485,0.006212073,0.006212073,0.006212073,0.006212073,0.006524027,0.006760143,0.006760143,0.007247225,0.007302696,0.00745667,0.007540015,0.010006453,0.010711752,0.012223333,0.012223333,0.01383456,0.014768421,0.014866079,0.01495666,0.016387919,0.016387919,0.016399233,0.016399233,0.016399233,0.020236508,0.020357536,0.020357536,0.021222655,0.021222655,0.021880568,0.022493145,0.022668597,0.023257588,0.024246409,0.024246409,0.024611334,0.02501158,0.02501158,0.028996112,0.029529916,0.029529916,0.029612423,0.03013124,0.03013124,0.031798869,0.035145943,0.035166079,0.035166079,0.036048176,0.036079466,0.038971488,0.03979543,0.040820823,0.043375426,0.044479277,0.047088372)

psc1$genelist <- data.frame(ID,log2FC,q.val)

head(psc1$genelist)
       ID   log2FC       q.val
1  UBE2L6 4.912166 0.000628860
2   IFIT1 6.655473 0.001743489
3 S100A14 2.375439 0.001946228
4   IFIT5 4.209728 0.002447293
5   RSAD2 1.722467 0.002710500
6   ISG15 2.049069 0.003306247

library(GOplot)

circ <- circle_dat(psc1$david, psc1$genelist)
  

总和(值)错误:无效&#39;输入&#39;参数(列表)

0 个答案:

没有答案