rDGIdb package: score of the results
0
0
Entering edit mode
HELEN • 0
@ba287559
Last seen 13 months ago
Greece

Hello, i run the code that is for the rDGIDB data base and i want to see also the scores from the gene-drug relation. But in the results the scores don't appear. Neither of the functions result give the result of the scores.
I run the code above.

library(rDGIdb)
mygenes <- c("MYD88", "FGFR3", "CCND1", "TP53", "MIR19A","MYOM2", "KRAS", "MIR32",
            "MIR106B", "MIR93", "MIR181A2", "MIR25", "MYC", "MIR15A", "DKK1", 
            "LIG4", "TNFSF11", "UBA1", "U2AF1", "SDC1", "IRF4", "B2M", "STOML2", 
            "IL6", "MAG", "NCAM1", "NSD2", "ALB", "CCND3", "CD19", "CCR6", "PTPRC", 
            "TNFRSF17", "TNFSF13B", "CCL3", "CD27", "CD38", "CD8A", "CKS1B", 
            "MAF", "CRBN", "DIS3", "ICOSLG", "MIR126", "TNFRSF11B", "CD36",
            "MAFB", "SLAMF7", "CFHR2", "TENT5C", "MIR30D", "IGHV4-38-2", "RB1", 
            "STAT3", "EPO", "CD40LG", "CDKN2B", "IL6R", "DNMT3A", "TET2", "KIT",
            "TRIM31", "IGHM", "MICA", "ENTPD1", "KLRK1", "SPP1", "CALR", "TOP1",
            "CANX", "TAPBP", "VEGFA", "NBEA", "CXCR4", "EPOR", "ICAM1", "IL1B", 
            "VCAM1", "PPP2R2B", "TPP2", "HGF", "IL4", "NRAS", "TNFRSF11A", "FGF2", 
            "XBP1", "CDKN2C", "CSF1", "TNFSF10", "LTA", "IL3", "CD58", "MET",
            "JAK2", "BCL2", "FASLG", "BGLAP", "MIR21", "CD40", "ITGB1", "CXCL12",
            "CSF3", "MIR17", "MIR181A1", "IGHG1", "AKT1", "CASP8", "HRAS", "ABCB1", 
            "FN1", "CCND2", "CDKN1A", "IGF1", "ITGAL", "IL7R", "CD47", "JAG2",
            "IFNA2", "IL7", "FCGR1A", "CTAG1B", "PVT1", "MALAT1", "MIR342",
            "LECT2", "NOTCH1", "PARP1", "FAS", "CD79A", "ITGAM", "HPSE", "CDKN2A",
            "ASXL1", "MAPRE2", "PIGA", "UBA7", "ENAM", "FAM83H", "ZRSR2", "TPPP2",
            "IGH", "TP73", "RASSF1", "SOCS1", "MTOR", "CDK4", "IGF1R", "IKBKB",
            "PTPN11", "ATM", "BRAF", "CREBBP", "FLT3", "IDH1", "IDH2", "JAK1",
            "NTRK2", "STAT1", "TYK2", "HDAC4", "MAPK1", "NFKB2", "PIK3CA", "XIAP",
            "CDK2", "CHUK", "HSP90AA1", "TFRC", "AURKA", "BAX", "ITGB2", "MAPK8",
            "NFKBIA", "TNFRSF10B", "TNFRSF1A", "BDNF", "CASP3", "HDAC9", "IL6ST", 
            "ITGA5", "MST1R", "NR3C1", "PIK3R2", "RXRA", "SGK1", "BCL2L1", "CD28",
            "CD44", "CYCS", "CYLD", "HSPA5", "ITGA4", "LYN", "MCL1", "STAT5A",
            "YAP1", "BAP1", "CD79B", "NF1", "SH2B3", "ACP5", "BARD1", "BIRC2",
            "BIRC3", "CASP9", "DIABLO", "IL2", "KDM5C", "KITLG", "NKX2-1",
            "TNFRSF13B", "TRAF3", "ANXA5", "BAK1", "BCL2L11", "BCL6", "BIRC5",
            "CD33", "CUBN", "DDIT3", "HLA-B", "PAX5", "PTHLH", "TCF3", "TNFRSF10A",
            "CD80", "CD86", "CD9", "CFLAR", "CSF2", "KMT2C", "LATS1", "PRDM1",
            "SFRP1", "VTN", "HBEGF", "HMMR", "KMT2D", "LIF", "NCOR2", "OSM",
            "SAMHD1", "TNFRSF8", "H1-4", "IL15", "TCL1A", "TRNT1", "CXCR5",
            "EIF1AX", "ERF", "KDM4C", "TET3", "BBC3", "BCL2A1", "CCL4", "IL11", 
            "RECQL4", "SFRP2", "TNFRSF10C", "TRAF5", "FAT1", "ARID4A", "IFNA1", 
            "H3C1", "DAZAP2", "MGA", "P2RY8", "LRRC56", "SPA17", "BCORL1", 
            "FAM135A", "H2AC16", "H2AC17", "MYEOV", "SFTA3", "H2AC18", "MEG3", 
            "H19", "HOTAIR", "GAS5", "MIR140", "MIR145", "MIR27A", "TP73-AS1",
            "TUG1", "UCA1", "MIR142", "MIR125A", "MIR155", "MIR221", "MIR9-1",
            "MIR199A1", "MIR335", "MIR99B", "MIRLET7B", "MIRLET7E", "MIR561",
            "PCAT1", "ST3GAL6-AS1", "TET2-AS1", "CCAT1", "LAMA5-AS1", "PDIA3P1",
            "TNF", "DAPK1", "CDH1", "PTPN6", "ANGPT2", "ANGPT1", "TKT", "ACP1",
            "MGMT", "CDKN1B", "SIL1", "HAS1", "IL1A", "LCN1", "MAGEC1", "CTLA4",
            "CD274", "PF4", "ESM1", "KDR", "CRP", "SOX2", "TANK", "TERF1", 
            "TERF2", "RARB", "EDN1", "MLH1", "IGFBP3", "INS", "DCC", "DLAT",
            "SEMA3A", "THBS1", "IGFBP2", "TIMP3", "CCL20", "POT1", "CTAG2", 
            "MIR214", "MIR27B", "SLC2A1", "ITGB3", "GSTP1", "IFNG", "GCK", 
            "PRKAG2", "SYK", "HIF1A", "VCL", "AQP1", "ACADM", "FOXP1", "FOXP2", 
            "H2AX", "HLA-G", "LILRB1", "POSTN", "PTX3", "TP53BP1", "LAG3", "IBSP", 
            "MAGEA3", "MIR203A", "MIR181B1", "MIR129-2", "MIR19B1", "MIR19B2",
            "MIR1258", "MMP9", "CTSB", "CTSD", "ELANE", "SRC", "TEK", "SHH",
            "CASP1", "COL1A1", "COL2A1", "FGA", "KDM1A", "PTGS2", "RAD50",
            "SERPINA1", "BRD4", "CASP10", "COL4A1", "ENG", "FGG", "MMP8", "MRE11",
            "PDCD1", "ANXA1", "COL1A2", "COL3A1", "CTSC", "DCN", "GP1BA", "NRP1",
            "COL4A2", "COL4A3", "COL5A1", "DKC1", "F13A1", "FGB", "FOXP3", "RPA1", 
            "THBS2", "C1QC", "COL6A2", "CTSG", "CTSS", "CTSZ", "FGF23", "HRG",
            "LCN2", "LGALS3", "PLXNA1", "SPRY2", "TNFRSF13C", "ARNT", "BSG",
            "COL17A1", "COL4A5", "COL4A6", "COL5A2", "CR1", "CST3", "ADAM19", 
            "ANXA11", "COL11A2", "COL7A1", "GYPA", "S100A9", "SERPINA3", "ZP3",
            "ANXA6", "CD5", "SERPINB6", "SERPINB8", "COL10A1", "FLG", "S100A8",
            "BNIP3", "CCN1", "CCT3", "CD200", "COL27A1", "CXCL13", "FCN1", "MANF", 
            "PECAM1", "PRG2", "SERPINB1", "CLC", "DIO2", "EVL", "SERPINB9", 
            "COL16A1", "COL5A3", "HMCN1", "SAMSN1", "MMP23B", "PRAME", "PRG3", 
            "MAGEA4", "COL6A5", "HRNR", "MAGEA10", "MUC17", "MAGEC2", "LMLN",
            "SSX2", "MXRA5", "SSX5", "IL2RA", "CHEK1", "EGLN1", "GBA1", "HSP90AB1", 
            "IL2RB", "TPO", "MECOM", "EGLN3", "IDO1", "IGFBP7", "ADIPOQ", "F3", 
            "LIG3", "UBE2D3", "ADM", "CHI3L1", "TG", "IL17A", "SCYL1", "LIN28B",
            "UBE2O", "CXCL9", "LY9", "OTUD6B", "PTP4A3", "SIVA1", "MIR107",
            "MIR134", "LOC106627981")
result <- queryDGIdb(genes = mygenes)

myresultspartb <-resultSummary(result)
myresultspartc <-byGene(result)
myresultspartd <-searchTermSummary(result)

myresults <-detailedResults(result)

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253    LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C                 
[5] LC_TIME=Greek_Greece.1253    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rDGIdb_1.20.0

loaded via a namespace (and not attached):
[1] httr_1.4.4        compiler_4.1.2    R6_2.5.1          cli_3.6.0         tools_4.1.2       jsonlite_1.8.4   
[7] sessioninfo_1.2.2
rDGIdb r • 464 views
ADD COMMENT

Login before adding your answer.

Traffic: 905 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6