raph06
commented
6 years ago Hello,
This error arises from a wrong column annotation (log2FC) in your psc1$genelist object. column name should be "logFC"
You can also try to run the function found in the following link step by step if any more error arise.
https://github.com/wencke/wencke.github.io/blob/91963feeaf4847f1ccff049511fb230eac153cc2/R/GOCore.R (lfc error line 60)
Best Raphael
Nice package btw..
Dear Wencke, Please could you help me?
category <- rep("BP",8)
ID <- c("GO:0016032","GO:0043207","GO:0045087","GO:0002252","GO:0051607","GO:0034097","GO:0050792","GO:0045088")
Term <- c("Viral process","Response to external biotic stimulus","Innate immune response","Immune effector process","Defense response to virus","Response to cytokine","Regulation of viral process","Regulation of innate immune response")
Genes <- c("BATF2, NMI, BST2, CXCL9, TRIM14, RSAD2, OAS2, STAT1, CCL5, S100A14, TRIM21, CXCL10, DDX58, OASL, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58","NMI, CXCL9, TRIM14, RSAD2, OAS2, STAT1, CCL5, S100A14, TRIM21, CXCL10, DDX58, OASL, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58","BST2, CXCL9, TRIM14, RSAD2, OAS2, CCL5, FURIN, TRIM21, CXCL10, DDX58, IFIT1, OASL, ISG15, MB21D1, MX2, DHX58 ","BATF2, BST2, CXCL9, RSAD2, OAS2, CCL5, S100A14, CMPK2, CXCL10, DDX58, OASL, IFIT1, ISG15, MB21D1, MX2, DHX58","NMI, TRIM14, RSAD2, STAT1, CCL5, S100A14, TRIM21, DDX58, IFIT1, PARP9, ISG15, MB21D1, IRF7, MX2, DHX58","DDX58, OASL, IFIT1, BST2, ISG15, MB21D1, IRF7, CXCL9, RSAD2, OAS2, MX2, DHX58, CXCL10","DDX58, OASL, IFIT1, BST2, ISG15, MB21D1, CXCL9, RSAD2, OAS2, MX2, DHX58, CXCL10","IFIT1, NMI, PARP9, ISG15, IRF7, CXCL9, CCL5, STAT1, MX2, TRIM21, CXCL10")
q.val <- c(0.000000018,0.000000969,0.000000074,0.000146408,0.000000476,0.003476769,0.000063716,0.001187458)
psc1 <- vector()
psc1$david <- data.frame(category,ID,Term,Genes,q.val) Warning message: In psc1$david <- data.frame(category, ID, Term, Genes, q.val) : Coercing LHS to a list
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)
library(GOplot) circ <- circle_dat(psc1$david, psc1$genelist) Error in sum(value) : invalid 'type' (list) of argument
Please could you help me deal with this error? Thanks in advance.