rDGIdb package: score of the results
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@ba287559
Last seen 20 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 • 656 views
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