getEnrichmentTable-GreatObject-method.RdGet enrichment table
# S4 method for GreatObject
getEnrichmentTable(object, min_region_hits = 5)A GreatObject-class object returned by great.
Minimal number of input regions overlapping to the geneset associated regions.
Note: adjusted p-values are re-calculated based on min_region_hits.
A data frame of enrichment results
obj = readRDS(system.file("extdata", "GreatObject.rds", package = "rGREAT"))
getEnrichmentTable(obj)
#> id genome_fraction
#> 1 HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.024706189
#> 2 HALLMARK_INTERFERON_GAMMA_RESPONSE 0.016214887
#> 3 HALLMARK_P53_PATHWAY 0.016053003
#> 4 HALLMARK_DNA_REPAIR 0.008096888
#> 5 HALLMARK_ALLOGRAFT_REJECTION 0.016780458
#> 6 HALLMARK_MTORC1_SIGNALING 0.016315292
#> 7 HALLMARK_HYPOXIA 0.022581770
#> 8 HALLMARK_INTERFERON_ALPHA_RESPONSE 0.006328124
#> 9 HALLMARK_MYC_TARGETS_V2 0.002622415
#> 10 HALLMARK_IL6_JAK_STAT3_SIGNALING 0.005880370
#> 11 HALLMARK_IL2_STAT5_SIGNALING 0.021152759
#> 12 HALLMARK_MITOTIC_SPINDLE 0.018888605
#> 13 HALLMARK_MYC_TARGETS_V1 0.012596381
#> 14 HALLMARK_INFLAMMATORY_RESPONSE 0.021400596
#> 15 HALLMARK_HEME_METABOLISM 0.015341534
#> 16 HALLMARK_E2F_TARGETS 0.013430423
#> 17 HALLMARK_ESTROGEN_RESPONSE_LATE 0.019761793
#> 18 HALLMARK_UNFOLDED_PROTEIN_RESPONSE 0.007310811
#> 19 HALLMARK_APOPTOSIS 0.015572219
#> 20 HALLMARK_TGF_BETA_SIGNALING 0.007151801
#> 21 HALLMARK_UV_RESPONSE_UP 0.014216156
#> 22 HALLMARK_XENOBIOTIC_METABOLISM 0.013703369
#> 23 HALLMARK_PI3K_AKT_MTOR_SIGNALING 0.009304123
#> 24 HALLMARK_G2M_CHECKPOINT 0.019536864
#> 25 HALLMARK_WNT_BETA_CATENIN_SIGNALING 0.005978667
#> 26 HALLMARK_ADIPOGENESIS 0.014848629
#> 27 HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY 0.003293391
#> 28 HALLMARK_COMPLEMENT 0.017884263
#> 29 HALLMARK_FATTY_ACID_METABOLISM 0.011573276
#> 30 HALLMARK_PEROXISOME 0.008096627
#> 31 HALLMARK_PROTEIN_SECRETION 0.009545438
#> 32 HALLMARK_NOTCH_SIGNALING 0.004362688
#> 33 HALLMARK_ESTROGEN_RESPONSE_EARLY 0.024463198
#> 34 HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.012476423
#> 35 HALLMARK_CHOLESTEROL_HOMEOSTASIS 0.006643875
#> 36 HALLMARK_ANDROGEN_RESPONSE 0.011675914
#> 37 HALLMARK_GLYCOLYSIS 0.019396858
#> 38 HALLMARK_MYOGENESIS 0.018892268
#> 39 HALLMARK_SPERMATOGENESIS 0.013961320
#> 40 HALLMARK_BILE_ACID_METABOLISM 0.010040486
#> 41 HALLMARK_KRAS_SIGNALING_UP 0.028175863
#> 42 HALLMARK_APICAL_SURFACE 0.005550360
#> 43 HALLMARK_COAGULATION 0.010231163
#> 44 HALLMARK_UV_RESPONSE_DN 0.029062603
#> 45 HALLMARK_PANCREAS_BETA_CELLS 0.005771070
#> 46 HALLMARK_ANGIOGENESIS 0.004438923
#> 47 HALLMARK_HEDGEHOG_SIGNALING 0.006965189
#> 48 HALLMARK_APICAL_JUNCTION 0.019630129
#> 49 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.030187448
#> 50 HALLMARK_KRAS_SIGNALING_DN 0.021228253
#> observed_region_hits fold_enrichment p_value p_adjust mean_tss_dist
#> 1 225 2.4298372 0.000000e+00 0.000000e+00 136782
#> 2 139 2.2871850 0.000000e+00 0.000000e+00 110305
#> 3 137 2.2770087 0.000000e+00 0.000000e+00 94877
#> 4 78 2.5702591 2.805534e-13 3.506917e-12 102965
#> 5 124 1.9715977 4.112710e-12 4.112710e-11 109342
#> 6 116 1.8969835 1.875065e-10 1.562554e-09 71572
#> 7 145 1.7132094 9.682692e-10 6.916209e-09 154740
#> 8 58 2.4454199 1.717376e-09 1.073360e-08 73640
#> 9 32 3.2557345 1.566151e-08 8.700838e-08 22648
#> 10 52 2.3593867 3.516391e-08 1.758196e-07 112002
#> 11 131 1.6523601 4.605719e-08 2.093509e-07 107985
#> 12 117 1.6526709 2.334794e-07 9.728310e-07 92190
#> 13 85 1.8004188 3.937057e-07 1.514253e-06 42520
#> 14 124 1.5459528 2.702549e-06 9.651962e-06 73325
#> 15 91 1.5826068 2.367115e-05 7.890385e-05 111452
#> 16 81 1.6091471 3.751312e-05 1.172285e-04 24539
#> 17 110 1.4851378 4.754000e-05 1.398235e-04 113146
#> 18 49 1.7882612 1.182907e-04 3.285853e-04 76815
#> 19 85 1.4563603 5.712321e-04 1.503242e-03 75367
#> 20 45 1.6787943 7.862261e-04 1.965565e-03 214758
#> 21 77 1.4451369 1.226371e-03 2.919930e-03 90633
#> 22 72 1.4018629 3.535443e-03 8.035098e-03 82734
#> 23 52 1.4911740 3.819475e-03 8.303206e-03 79961
#> 24 92 1.2564158 1.807399e-02 3.765415e-02 89868
#> 25 33 1.4726854 2.088977e-02 4.177953e-02 144703
#> 26 71 1.2757701 2.577342e-02 4.956427e-02 72626
#> 27 20 1.6202691 2.718872e-02 5.034948e-02 41506
#> 28 83 1.2382475 3.144824e-02 5.615757e-02 87133
#> 29 56 1.2910175 3.602869e-02 6.135155e-02 99736
#> 30 41 1.3510772 3.681093e-02 6.135155e-02 123711
#> 31 47 1.3137189 4.021162e-02 6.485745e-02 84906
#> 32 24 1.4677682 4.449403e-02 6.952192e-02 210461
#> 33 106 1.1560938 7.449392e-02 1.128696e-01 124126
#> 34 57 1.2189480 7.912587e-02 1.163616e-01 49573
#> 35 29 1.1646006 2.297476e-01 3.220774e-01 120463
#> 36 49 1.1197102 2.318957e-01 3.220774e-01 115681
#> 37 78 1.0729108 2.804896e-01 3.714439e-01 112176
#> 38 76 1.0733217 2.822974e-01 3.714439e-01 126440
#> 39 55 1.0510821 3.733741e-01 4.786848e-01 153792
#> 40 38 1.0097859 4.979006e-01 6.223757e-01 165115
#> 41 104 0.9848192 5.763953e-01 7.029211e-01 166240
#> 42 18 0.8652702 7.608707e-01 9.057985e-01 313183
#> 43 33 0.8605762 8.282246e-01 9.630519e-01 141944
#> 44 97 0.8905076 8.880386e-01 1.000000e+00 180934
#> 45 16 0.7397144 9.122784e-01 1.000000e+00 185369
#> 46 11 0.6611735 9.422727e-01 1.000000e+00 185013
#> 47 17 0.6512031 9.766420e-01 1.000000e+00 103191
#> 48 46 0.6252232 9.997948e-01 1.000000e+00 94333
#> 49 58 0.5126276 1.000000e+00 1.000000e+00 170607
#> 50 28 0.3519202 1.000000e+00 1.000000e+00 162931
#> observed_gene_hits gene_set_size fold_enrichment_hyper p_value_hyper
#> 1 96 197 2.3768986 0.000000e+00
#> 2 68 189 1.7549015 5.532986e-07
#> 3 74 197 1.8321926 2.319365e-08
#> 4 41 148 1.3512253 2.164514e-02
#> 5 63 186 1.6520883 1.359518e-05
#> 6 57 200 1.3901143 4.178830e-03
#> 7 66 199 1.6176945 1.858699e-05
#> 8 30 92 1.5905198 4.331584e-03
#> 9 22 58 1.8501218 1.690956e-03
#> 10 30 81 1.8065163 4.342800e-04
#> 11 64 196 1.5926837 4.227029e-05
#> 12 63 198 1.5519617 1.130186e-04
#> 13 58 197 1.4360429 1.749116e-03
#> 14 72 197 1.7826739 1.281090e-07
#> 15 51 197 1.2627274 3.913441e-02
#> 16 49 198 1.2070813 8.304502e-02
#> 17 53 198 1.3056186 1.986565e-02
#> 18 31 112 1.3500483 4.192685e-02
#> 19 53 158 1.6361549 8.441453e-05
#> 20 22 54 1.9871679 5.489573e-04
#> 21 44 154 1.3935983 1.032754e-02
#> 22 42 197 1.0398931 4.154699e-01
#> 23 28 104 1.3131984 6.948869e-02
#> 24 55 197 1.3617648 7.603210e-03
#> 25 18 41 2.1413827 5.959418e-04
#> 26 46 200 1.1218466 2.123926e-01
#> 27 15 49 1.4931410 6.204395e-02
#> 28 49 195 1.2256518 6.684081e-02
#> 29 34 157 1.0562942 3.904179e-01
#> 30 20 104 0.9379988 6.642766e-01
#> 31 28 95 1.4376066 2.386293e-02
#> 32 11 32 1.6766729 4.807732e-02
#> 33 48 198 1.1824470 1.121858e-01
#> 34 48 199 1.1765051 1.195536e-01
#> 35 17 74 1.1205283 3.419974e-01
#> 36 30 100 1.4632782 1.552103e-02
#> 37 51 199 1.2500366 4.610945e-02
#> 38 37 200 0.9023549 7.842976e-01
#> 39 32 134 1.1647985 1.920403e-01
#> 40 24 112 1.0451987 4.408976e-01
#> 41 50 197 1.2379680 5.565732e-02
#> 42 10 44 1.1085441 4.150620e-01
#> 43 19 136 0.6814286 9.810608e-01
#> 44 45 143 1.5349072 1.291134e-03
#> 45 11 40 1.3413383 1.814494e-01
#> 46 5 36 0.6774436 8.876329e-01
#> 47 11 36 1.4903759 1.021387e-01
#> 48 35 196 0.8709989 8.441815e-01
#> 49 38 199 0.9313998 7.159596e-01
#> 50 19 198 0.4680519 9.999893e-01
#> p_adjust_hyper
#> 1 0.000000e+00
#> 2 6.916232e-06
#> 3 5.798413e-07
#> 4 4.919350e-02
#> 5 1.359518e-04
#> 6 1.273995e-02
#> 7 1.548915e-04
#> 8 1.273995e-02
#> 9 5.830387e-03
#> 10 2.171400e-03
#> 11 3.019306e-04
#> 12 6.278812e-04
#> 13 5.830387e-03
#> 14 2.135150e-06
#> 15 8.153001e-02
#> 16 1.297579e-01
#> 17 4.729916e-02
#> 18 8.385370e-02
#> 19 5.275908e-04
#> 20 2.483091e-03
#> 21 2.717774e-02
#> 22 4.946070e-01
#> 23 1.120785e-01
#> 24 2.112003e-02
#> 25 2.483091e-03
#> 26 2.794639e-01
#> 27 1.069723e-01
#> 28 1.114014e-01
#> 29 4.880224e-01
#> 30 7.548598e-01
#> 31 5.187594e-02
#> 32 8.903207e-02
#> 33 1.649791e-01
#> 34 1.707909e-01
#> 35 4.384583e-01
#> 36 3.880257e-02
#> 37 8.867202e-02
#> 38 8.524974e-01
#> 39 2.595139e-01
#> 40 5.126716e-01
#> 41 9.938808e-02
#> 42 4.946070e-01
#> 43 9.999893e-01
#> 44 4.965898e-03
#> 45 2.520130e-01
#> 46 9.246176e-01
#> 47 1.547556e-01
#> 48 8.980654e-01
#> 49 7.955107e-01
#> 50 9.999893e-01