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 -0.4953723732
#> 2: 51 41 9 32 11 30 0 9 -0.7685127185
#> 3: 51 50 9 41 14 36 1 8 -0.7654912267
#> 4: 9 6 0 6 1 5 0 0 -0.2319652336
#> 5: 23 23 2 21 14 9 2 0 0.3419175833
#> 6: 50 45 7 38 13 32 0 7 -0.4568978729
#> 7: 12 12 1 11 6 6 1 0 -0.0110327774
#> 8: 32 26 3 23 10 16 0 3 -0.4563743726
#> 9: 781 699 70 629 344 355 8 62 -0.0009819938
#> 10: 9 9 2 7 2 7 0 2 -0.6026479280
#> 11: 20 19 0 19 9 10 0 0 -0.0913120066
#> 12: 54 52 9 43 15 37 1 8 -0.6465575653
#> 13: 9 9 1 8 3 6 0 1 -0.3442783567
#> 14: 14 14 8 6 14 0 8 0 1.9053048170
#> 15: 8 8 2 6 3 5 0 2 -0.5900503448
#> 16: 172 170 10 160 104 66 6 4 0.1972357423
#> 17: 16 14 0 14 10 4 0 0 0.2011107549
#> 18: 56 55 18 37 47 8 18 0 1.0281692628
#> 19: 27 18 2 16 10 8 1 1 0.3092422557
#> 20: 205 109 14 95 53 56 3 11 -0.0985714855
#> 21: 45 42 2 40 35 7 2 0 0.3510180096
#> 22: 10 10 1 9 8 2 1 0 0.4230694131
#> 23: 33 33 1 32 19 14 1 0 0.1036578463
#> 24: 428 356 63 293 137 219 5 58 -0.3405690573
#> 25: 151 149 80 69 147 2 80 0 1.8402358512
#> 26: 7 7 0 7 3 4 0 0 -0.0906006930
#> 27: 91 91 20 71 24 67 0 20 -0.9569426993
#> 28: 240 233 28 205 135 98 20 8 0.2188469979
#> 29: 76 47 5 42 16 31 0 5 -0.5284610949
#> 30: 79 75 5 70 40 35 3 2 0.0871837606
#> 31: 146 89 13 76 29 60 1 12 -0.4379006826
#> 32: 100 42 10 32 20 22 3 7 -0.0078142129
#> 33: 200 183 22 161 75 108 2 20 -0.2631504959
#> 34: 130 99 13 86 44 55 2 11 -0.2898176715
#> 35: 191 157 14 143 75 82 5 9 -0.0835959840
#> 36: 188 148 22 126 80 68 4 18 -0.1562322733
#> 37: 193 142 11 131 60 82 4 7 -0.0757932566
#> 38: 196 155 21 134 98 57 9 12 0.2605312569
#> 39: 196 186 21 165 89 97 8 13 0.1124195286
#> 40: 191 179 19 160 90 89 2 17 0.0423165304
#> 41: 169 135 15 120 63 72 3 12 -0.1129057892
#> 42: 29 24 0 24 19 5 0 0 0.1548457256
#> 43: 48 33 10 23 9 24 2 8 -0.5773156100
#> 44: 289 189 23 166 77 112 1 22 -0.3056071153
#> 45: 288 163 29 134 69 94 7 22 -0.2619302521
#> 46: 145 90 9 81 31 59 0 9 -0.3264680368
#> 47: 146 74 12 62 30 44 1 11 -0.2928758361
#> 48: 194 146 16 130 55 91 2 14 -0.2162652245
#> 49: 145 96 11 85 36 60 1 10 -0.3470210371
#> 50: 145 84 13 71 36 48 3 10 -0.2984086235
#> 51: 145 98 13 85 34 64 1 12 -0.4812555290
#> 52: 196 187 18 169 89 98 1 17 -0.1270971524
#> 53: 148 125 17 108 48 77 1 16 -0.3763351982
#> 54: 179 132 13 119 72 60 6 7 0.1247434888
#> 55: 287 278 14 264 151 127 4 10 -0.0011542493
#> 56: 50 50 7 43 31 19 5 2 0.2699207701
#> 57: 200 165 13 152 89 76 4 9 -0.0023415431
#> 58: 200 177 13 164 72 105 3 10 -0.1575295984
#> 59: 200 181 10 171 111 70 2 8 0.0596145477
#> 60: 200 191 11 180 130 61 4 7 0.2774771952
#> 61: 200 192 9 183 95 97 1 8 -0.0632012058
#> 62: 199 188 9 179 112 76 6 3 0.1426046332
#> 63: 200 186 20 166 82 104 2 18 -0.1692316475
#> 64: 200 186 10 176 110 76 4 6 0.1403832130
#> 65: 200 167 13 154 94 73 5 8 0.0481487837
#> 66: 200 181 19 162 90 91 4 15 -0.0707097113
#> 67: 200 176 17 159 57 119 0 17 -0.3241097399
#> 68: 200 195 13 182 94 101 2 11 -0.0520041142
#> 69: 200 191 7 184 105 86 4 3 0.0789238288
#> 70: 200 171 20 151 61 110 4 16 -0.1297963535
#> 71: 200 196 15 181 114 82 8 7 0.1000431016
#> 72: 200 177 9 168 98 79 5 4 0.0590716982
#> 73: 200 102 10 92 46 56 1 9 -0.2524930750
#> 74: 200 175 30 145 116 59 20 10 0.3908601854
#> 75: 200 143 6 137 64 79 2 4 0.0291063997
#> 76: 200 186 19 167 87 99 3 16 -0.1147572914
#> 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: -0.504456566 -1.3726440924 -1.37656140
#> 2: -0.650047409 -1.5021451144 -1.52125651
#> 3: -0.738211807 -1.0964370005 -1.15640608
#> 4: -0.231965234 -0.5767634874 -0.57676349
#> 5: 0.213996440 0.6136099258 0.43342914
#> 6: -0.471149298 -1.1350462109 -1.06810360
#> 7: -0.021924426 0.1194276997 0.06518866
#> 8: -0.393514406 -0.8407864711 -0.78651129
#> 9: -0.017191121 -0.2665663699 -0.14849338
#> 10: -0.602647928 -1.7435775019 -1.74357750
#> 11: -0.088585764 -0.4247283989 -0.39204388
#> 12: -0.756699312 -1.0664421197 -1.04814881
#> 13: -0.344278357 -0.8135939005 -0.81359390
#> 14: 1.920195685 2.6611296153 2.72294131
#> 15: -0.590050345 -0.9610152820 -0.96101528
#> 16: 0.168508918 0.5338253634 0.57811997
#> 17: 0.188288741 0.2788266318 0.35250365
#> 18: 0.953301553 1.7020743730 1.81773601
#> 19: 0.295278296 0.2252134153 0.29685363
#> 20: -0.112177613 -0.3506613557 -0.26659562
#> 21: 0.343381369 1.2752434757 1.29598156
#> 22: 0.212870935 0.8176966400 0.73650528
#> 23: 0.102550698 0.4105173700 0.37148089
#> 24: -0.326827342 -0.7889832298 -0.70503035
#> 25: 1.831099299 2.8107308266 2.87156246
#> 26: -0.090600693 -0.3800829397 -0.38008294
#> 27: -0.938714170 -1.3803431574 -1.23973135
#> 28: 0.153104853 0.2752792156 0.29280132
#> 29: -0.436960281 -0.8993548923 -0.82070498
#> 30: 0.064534822 0.2152850586 0.24033608
#> 31: -0.411716175 -0.7610840215 -0.74353242
#> 32: -0.006877086 -0.1384287870 -0.20952520
#> 33: -0.230687421 -0.6154836015 -0.58001351
#> 34: -0.205999028 -0.4517751984 -0.35395534
#> 35: -0.080559381 -0.2813232527 -0.24817415
#> 36: -0.081682479 -0.2756933971 -0.19091570
#> 37: -0.104354237 -0.2380874628 -0.26079041
#> 38: 0.289617009 0.3003986200 0.39536626
#> 39: 0.036104082 -0.0835266650 -0.01704386
#> 40: -0.026297271 -0.3358874983 -0.22844514
#> 41: -0.061615121 -0.3596354028 -0.22443311
#> 42: 0.181004145 0.5389948734 0.64552542
#> 43: -0.672507959 -0.9812401468 -1.15459699
#> 44: -0.262763783 -0.6498983573 -0.51449619
#> 45: -0.293746242 -0.5636593981 -0.57181382
#> 46: -0.309888724 -0.7466724945 -0.58918672
#> 47: -0.318158761 -0.6840203276 -0.59413972
#> 48: -0.186696815 -0.4579948360 -0.37818956
#> 49: -0.339655885 -0.7333986197 -0.61494642
#> 50: -0.384475852 -0.6379883189 -0.61440638
#> 51: -0.430913814 -0.7247245622 -0.61597825
#> 52: -0.087742640 -0.2820683824 -0.17385407
#> 53: -0.352485482 -0.6472540045 -0.55274799
#> 54: 0.057129032 0.0517123272 0.12236453
#> 55: 0.022088459 0.0004562912 0.07316595
#> 56: 0.165872449 0.4860195552 0.52282625
#> 57: 0.031168729 0.0661749124 0.15306700
#> 58: -0.134924951 -0.4791426791 -0.44117642
#> 59: 0.128639941 0.2686249866 0.38617388
#> 60: 0.268524219 0.4590223633 0.58219295
#> 61: -0.026478909 -0.1812580428 -0.08712373
#> 62: 0.098029899 0.2767914081 0.29897039
#> 63: -0.096197648 -0.3444668517 -0.27231184
#> 64: 0.132598999 0.2295234996 0.30824886
#> 65: 0.092765614 0.1342282688 0.22171045
#> 66: -0.032733282 -0.2094416833 -0.14575970
#> 67: -0.289094627 -0.8570488456 -0.75816191
#> 68: -0.017071815 -0.2464366244 -0.14772799
#> 69: 0.074419210 0.1766810372 0.19708133
#> 70: -0.160887493 -0.6143383799 -0.58455832
#> 71: 0.072734385 0.1888241411 0.23655347
#> 72: 0.046705810 0.1583776365 0.18260813
#> 73: -0.189697337 -0.4459099712 -0.42500799
#> 74: 0.333794420 0.6218070770 0.71462689
#> 75: -0.035099478 -0.1273012191 -0.10689086
#> 76: -0.101640385 -0.4135795483 -0.36256203
#> mean.logFC.trim mean.t mean.t.trim
#> ---------------------------------------------------------------------------------
#> GeneSetDb with 76 defined genesets across 3 collections (76 gene sets are active)
#> Conformed: yes
#> =================================================================================