R/SparrowResult-methods.R
SparrowResult-utilities.RdFetches the GeneSetDb from SparrowResult
geneSetDb(x)The GeneSetDb
vm <- exampleExpressionSet(do.voom=TRUE)
gdb <- exampleGeneSetDb()
mg <- seas(vm, gdb, design = vm$design, contrast = 'tumor')
geneSetDb(mg)
#> =================================================================================
#> GeneSetDb with 76 defined genesets across 3 collections (76 gene sets are active)
#> Conformed: yes
#> ---------------------------------------------------------------------------------
#> Key: <collection, name>
#> collection name active
#> <char> <char> <lgcl>
#> 1: c2 BIOCARTA_AGPCR_PATHWAY TRUE
#> 2: c2 BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN TRUE
#> 3: c2 BURTON_ADIPOGENESIS_PEAK_AT_2HR TRUE
#> 4: c2 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA TRUE
#> 5: c2 CAIRO_PML_TARGETS_BOUND_BY_MYC_UP TRUE
#> 6: c2 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN TRUE
#> 7: c2 CLAUS_PGR_POSITIVE_MENINGIOMA_DN TRUE
#> 8: c2 DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_DN TRUE
#> 9: c2 GOZGIT_ESR1_TARGETS_DN TRUE
#> 10: c2 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_UP TRUE
#> 11: c2 HEDENFALK_BREAST_CANCER_BRACX_DN TRUE
#> 12: c2 HUPER_BREAST_BASAL_VS_LUMINAL_UP TRUE
#> 13: c2 KOMMAGANI_TP63_GAMMA_TARGETS TRUE
#> 14: c2 LOPEZ_MESOTELIOMA_SURVIVAL_TIME_UP TRUE
#> 15: c2 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_2 TRUE
#> 16: c2 MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN TRUE
#> 17: c2 NIKOLSKY_BREAST_CANCER_21Q22_AMPLICON TRUE
#> 18: c2 PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP TRUE
#> 19: c2 REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS TRUE
#> 20: c2 REACTOME_GASTRIN_CREB_SIGNALLING_PATHWAY_VIA_PKC_AND_MAPK TRUE
#> 21: c2 REACTOME_MRNA_SPLICING_MINOR_PATHWAY TRUE
#> 22: c2 REACTOME_RAF_MAP_KINASE_CASCADE TRUE
#> 23: c2 REACTOME_RNA_POL_III_TRANSCRIPTION TRUE
#> 24: c2 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN TRUE
#> 25: c2 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP TRUE
#> 26: c2 TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN TRUE
#> 27: c2 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN TRUE
#> 28: c2 VANTVEER_BREAST_CANCER_ESR1_DN TRUE
#> 29: c2 YAMASHITA_LIVER_CANCER_STEM_CELL_DN TRUE
#> 30: c2 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_12 TRUE
#> 31: c6 ATM_DN.V1_UP TRUE
#> 32: c6 CAHOY_NEURONAL TRUE
#> 33: c6 CAMP_UP.V1_DN TRUE
#> 34: c6 CRX_NRL_DN.V1_DN TRUE
#> 35: c6 CYCLIN_D1_UP.V1_DN TRUE
#> 36: c6 CYCLIN_D1_UP.V1_UP TRUE
#> 37: c6 DCA_UP.V1_DN TRUE
#> 38: c6 E2F3_UP.V1_UP TRUE
#> 39: c6 EGFR_UP.V1_DN TRUE
#> 40: c6 ERB2_UP.V1_UP TRUE
#> 41: c6 GCNP_SHH_UP_EARLY.V1_DN TRUE
#> 42: c6 GLI1_UP.V1_DN TRUE
#> 43: c6 KRAS.50_UP.V1_UP TRUE
#> 44: c6 KRAS.600.LUNG.BREAST_UP.V1_DN TRUE
#> 45: c6 KRAS.600.LUNG.BREAST_UP.V1_UP TRUE
#> 46: c6 KRAS.BREAST_UP.V1_DN TRUE
#> 47: c6 KRAS.BREAST_UP.V1_UP TRUE
#> 48: c6 KRAS.DF.V1_DN TRUE
#> 49: c6 KRAS.LUNG.BREAST_UP.V1_DN TRUE
#> 50: c6 KRAS.LUNG.BREAST_UP.V1_UP TRUE
#> 51: c6 KRAS.LUNG_UP.V1_DN TRUE
#> 52: c6 LTE2_UP.V1_DN TRUE
#> 53: c6 MEL18_DN.V1_DN TRUE
#> 54: c6 SRC_UP.V1_DN TRUE
#> 55: c6 TBK1.DF_DN TRUE
#> 56: c6 TBK1.DN.48HRS_DN TRUE
#> 57: c7 GSE12366_PLASMA_CELL_VS_MEMORY_BCELL_UP TRUE
#> 58: c7 GSE12845_IGD_POS_BLOOD_VS_PRE_GC_TONSIL_BCELL_UP TRUE
#> 59: c7 GSE13411_NAIVE_VS_IGM_MEMORY_BCELL_DN TRUE
#> 60: c7 GSE13485_CTRL_VS_DAY3_YF17D_VACCINE_PBMC_DN TRUE
#> 61: c7 GSE14000_UNSTIM_VS_16H_LPS_DC_UP TRUE
#> 62: c7 GSE14308_TH2_VS_TH1_UP TRUE
#> 63: c7 GSE14769_UNSTIM_VS_120MIN_LPS_BMDM_DN TRUE
#> 64: c7 GSE15930_STIM_VS_STIM_AND_TRICHOSTATINA_48H_CD8_T_CELL_DN TRUE
#> 65: c7 GSE17721_CTRL_VS_POLYIC_12H_BMDM_DN TRUE
#> 66: c7 GSE17721_POLYIC_VS_GARDIQUIMOD_8H_BMDM_UP TRUE
#> 67: c7 GSE22886_IGG_IGA_MEMORY_BCELL_VS_BLOOD_PLASMA_CELL_UP TRUE
#> 68: c7 GSE22886_NAIVE_TCELL_VS_MONOCYTE_DN TRUE
#> 69: c7 GSE27786_CD4_TCELL_VS_ERYTHTROBLAST_UP TRUE
#> 70: c7 GSE29618_BCELL_VS_MDC_UP TRUE
#> 71: c7 GSE339_EX_VIVO_VS_IN_CULTURE_CD8POS_DC_UP TRUE
#> 72: c7 GSE360_CTRL_VS_B_MALAYI_HIGH_DOSE_MAC_UP TRUE
#> 73: c7 GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_DN TRUE
#> 74: c7 GSE3982_BCELL_VS_TH2_DN TRUE
#> 75: c7 GSE3982_MAC_VS_NEUTROPHIL_LPS_STIM_DN TRUE
#> 76: c7 GSE7852_TREG_VS_TCONV_LN_UP TRUE
#> collection name active
#> N n n.sig n.neutral n.up n.down n.sig.up n.sig.down mean.logFC
#> <int> <int> <int> <int> <int> <int> <int> <int> <num>
#> 1: 13 11 1 10 3 8 0 1 -0.4952772999
#> 2: 51 41 9 32 11 30 0 9 -0.7681384340
#> 3: 51 50 9 41 14 36 1 8 -0.7659035727
#> 4: 9 6 0 6 1 5 0 0 -0.2321045624
#> 5: 23 23 2 21 14 9 2 0 0.3430059342
#> 6: 50 45 7 38 13 32 0 7 -0.4558733848
#> 7: 12 12 1 11 6 6 1 0 -0.0113367728
#> 8: 32 26 3 23 10 16 0 3 -0.4555882484
#> 9: 781 699 70 629 345 354 8 62 -0.0009360566
#> 10: 9 9 2 7 2 7 0 2 -0.6020587860
#> 11: 20 19 0 19 9 10 0 0 -0.0911097019
#> 12: 54 52 9 43 15 37 1 8 -0.6464681978
#> 13: 9 9 1 8 3 6 0 1 -0.3444605457
#> 14: 14 14 8 6 14 0 8 0 1.9075157626
#> 15: 8 8 2 6 3 5 0 2 -0.5897629316
#> 16: 172 170 10 160 104 66 6 4 0.1972898221
#> 17: 16 14 0 14 10 4 0 0 0.2008962197
#> 18: 56 55 18 37 47 8 18 0 1.0287068891
#> 19: 27 18 2 16 10 8 1 1 0.3097700711
#> 20: 205 109 14 95 53 56 3 11 -0.0983946628
#> 21: 45 42 2 40 35 7 2 0 0.3512321005
#> 22: 10 10 1 9 8 2 1 0 0.4225228776
#> 23: 33 33 1 32 19 14 1 0 0.1036289758
#> 24: 428 356 62 294 137 219 5 57 -0.3400780565
#> 25: 151 149 80 69 147 2 80 0 1.8413640290
#> 26: 7 7 0 7 3 4 0 0 -0.0901135146
#> 27: 91 91 20 71 24 67 0 20 -0.9568663468
#> 28: 240 233 28 205 134 99 20 8 0.2190458621
#> 29: 76 47 5 42 16 31 0 5 -0.5280391959
#> 30: 79 75 5 70 40 35 3 2 0.0872781821
#> 31: 146 89 12 77 29 60 1 11 -0.4375109839
#> 32: 100 42 10 32 20 22 3 7 -0.0071677489
#> 33: 200 183 22 161 75 108 2 20 -0.2631497276
#> 34: 130 99 13 86 44 55 2 11 -0.2902491330
#> 35: 191 157 14 143 75 82 5 9 -0.0836507736
#> 36: 188 148 22 126 80 68 4 18 -0.1563345242
#> 37: 193 142 11 131 60 82 4 7 -0.0758936934
#> 38: 196 155 21 134 98 57 9 12 0.2604860115
#> 39: 196 186 21 165 89 97 8 13 0.1123379862
#> 40: 191 179 19 160 90 89 2 17 0.0423441772
#> 41: 169 135 15 120 63 72 3 12 -0.1129465691
#> 42: 29 24 0 24 19 5 0 0 0.1549457539
#> 43: 48 33 10 23 9 24 2 8 -0.5770607728
#> 44: 289 189 23 166 77 112 1 22 -0.3055359257
#> 45: 288 163 29 134 69 94 7 22 -0.2618329512
#> 46: 145 90 9 81 31 59 0 9 -0.3265484599
#> 47: 146 74 12 62 30 44 1 11 -0.2918296123
#> 48: 194 146 16 130 55 91 2 14 -0.2163438396
#> 49: 145 96 11 85 36 60 1 10 -0.3476774145
#> 50: 145 84 13 71 36 48 3 10 -0.2978827537
#> 51: 145 98 13 85 34 64 1 12 -0.4816017950
#> 52: 196 187 18 169 89 98 1 17 -0.1267696181
#> 53: 148 125 17 108 47 78 1 16 -0.3763970591
#> 54: 179 132 13 119 72 60 6 7 0.1249607920
#> 55: 287 278 14 264 151 127 4 10 -0.0012210868
#> 56: 50 50 7 43 31 19 5 2 0.2696146358
#> 57: 200 165 13 152 89 76 4 9 -0.0020590751
#> 58: 200 177 13 164 72 105 3 10 -0.1574967640
#> 59: 200 181 10 171 111 70 2 8 0.0596395681
#> 60: 200 191 11 180 130 61 4 7 0.2775314719
#> 61: 200 192 9 183 95 97 1 8 -0.0630854466
#> 62: 199 188 9 179 112 76 6 3 0.1426926933
#> 63: 200 186 20 166 82 104 2 18 -0.1691170433
#> 64: 200 186 10 176 110 76 4 6 0.1403637403
#> 65: 200 167 13 154 94 73 5 8 0.0481689800
#> 66: 200 181 19 162 90 91 4 15 -0.0705046527
#> 67: 200 176 17 159 57 119 0 17 -0.3242494483
#> 68: 200 195 13 182 94 101 2 11 -0.0519641043
#> 69: 200 191 7 184 105 86 4 3 0.0789195051
#> 70: 200 171 20 151 61 110 4 16 -0.1296766066
#> 71: 200 196 15 181 114 82 8 7 0.0999302917
#> 72: 200 177 8 169 98 79 5 3 0.0591865340
#> 73: 200 102 10 92 46 56 1 9 -0.2524977738
#> 74: 200 175 30 145 116 59 20 10 0.3910948218
#> 75: 200 143 6 137 64 79 2 4 0.0286742877
#> 76: 200 186 19 167 87 99 3 16 -0.1146063560
#> N n n.sig n.neutral n.up n.down n.sig.up n.sig.down mean.logFC
#> mean.logFC.trim mean.t mean.t.trim
#> <num> <num> <num>
#> 1: -0.504732495 -1.373452080 -1.37716538
#> 2: -0.649795612 -1.501187139 -1.51993732
#> 3: -0.738498426 -1.094266941 -1.15513059
#> 4: -0.232104562 -0.577041340 -0.57704134
#> 5: 0.215554407 0.614853909 0.43562765
#> 6: -0.470826631 -1.135159316 -1.06822847
#> 7: -0.021962874 0.119406540 0.06571880
#> 8: -0.393226586 -0.841461646 -0.78646448
#> 9: -0.017217606 -0.267154483 -0.14907821
#> 10: -0.602058786 -1.743188270 -1.74318827
#> 11: -0.088337470 -0.422861313 -0.39015107
#> 12: -0.756659550 -1.067549612 -1.04906803
#> 13: -0.344460546 -0.814754526 -0.81475453
#> 14: 1.922224321 2.656214569 2.71752880
#> 15: -0.589762932 -0.955034454 -0.95503445
#> 16: 0.168590434 0.534125028 0.57857413
#> 17: 0.188282932 0.278105022 0.35169511
#> 18: 0.953786857 1.703776872 1.81994774
#> 19: 0.295524922 0.223095020 0.29377234
#> 20: -0.112574418 -0.351753447 -0.26814608
#> 21: 0.343632369 1.277257648 1.29783638
#> 22: 0.212599824 0.817660135 0.73691430
#> 23: 0.102525920 0.410449994 0.37158737
#> 24: -0.326603699 -0.789090303 -0.70457658
#> 25: 1.832171402 2.812008537 2.87283736
#> 26: -0.090113515 -0.379206618 -0.37920662
#> 27: -0.938814758 -1.378113218 -1.23819120
#> 28: 0.153138160 0.275585541 0.29314959
#> 29: -0.436723648 -0.898792490 -0.82048790
#> 30: 0.064581229 0.215466601 0.24048937
#> 31: -0.411634938 -0.759071066 -0.74211973
#> 32: -0.005792824 -0.145187382 -0.21198096
#> 33: -0.230894582 -0.614809711 -0.58015765
#> 34: -0.206552510 -0.452356377 -0.35434604
#> 35: -0.080914217 -0.280813577 -0.24867209
#> 36: -0.081908413 -0.274536064 -0.19099695
#> 37: -0.104408388 -0.239506872 -0.26077700
#> 38: 0.289451174 0.298260758 0.39204716
#> 39: 0.036140344 -0.085488881 -0.01785943
#> 40: -0.026440657 -0.336037643 -0.22894739
#> 41: -0.061689635 -0.360338130 -0.22495228
#> 42: 0.180925760 0.539536287 0.64517611
#> 43: -0.671866236 -0.978493842 -1.15180609
#> 44: -0.262603473 -0.650142819 -0.51456360
#> 45: -0.293672037 -0.564784378 -0.57208763
#> 46: -0.310306642 -0.748232708 -0.59081798
#> 47: -0.317075873 -0.687041826 -0.59404953
#> 48: -0.186830853 -0.458271754 -0.37890952
#> 49: -0.339635362 -0.733275699 -0.61528427
#> 50: -0.383927960 -0.638609264 -0.61367588
#> 51: -0.431162585 -0.724280130 -0.61582113
#> 52: -0.087583653 -0.282442898 -0.17434510
#> 53: -0.352640341 -0.645949160 -0.55072361
#> 54: 0.057177555 0.049085690 0.12090018
#> 55: 0.022019045 0.000461146 0.07291825
#> 56: 0.165621359 0.485049958 0.52244804
#> 57: 0.031472344 0.067169703 0.15388793
#> 58: -0.134863018 -0.478740404 -0.44099377
#> 59: 0.128635951 0.269523872 0.38666017
#> 60: 0.268476670 0.458376981 0.58079420
#> 61: -0.026339517 -0.180554940 -0.08639133
#> 62: 0.098064311 0.276829391 0.29878154
#> 63: -0.096081830 -0.343683275 -0.27257623
#> 64: 0.132636235 0.229515390 0.30786318
#> 65: 0.092799419 0.134586582 0.22206497
#> 66: -0.032685519 -0.208983839 -0.14565864
#> 67: -0.288977735 -0.856930387 -0.75788574
#> 68: -0.017141803 -0.246134208 -0.14804971
#> 69: 0.074362199 0.177217367 0.19714519
#> 70: -0.160841407 -0.614534801 -0.58503725
#> 71: 0.072665228 0.189027121 0.23661468
#> 72: 0.046702920 0.158611079 0.18238690
#> 73: -0.189924755 -0.446295930 -0.42520420
#> 74: 0.333757716 0.621132507 0.71429310
#> 75: -0.035062308 -0.128170988 -0.10776728
#> 76: -0.101572942 -0.413567744 -0.36248168
#> mean.logFC.trim mean.t mean.t.trim
#> ---------------------------------------------------------------------------------
#> GeneSetDb with 76 defined genesets across 3 collections (76 gene sets are active)
#> Conformed: yes
#> =================================================================================