constructGseaResultTable.RdCreates a table gene set statistics genereated from a GSEA `method` for all gene sets with an FDR (by collection) less than given threshold.
constructGseaResultTable(
mg,
method = sparrow::resultNames(mg)[1L],
fdr = 0.1,
prioritize = NULL
)`SparrowResult` object
the method to show statistics for
the FDR cut off to present statistics for
the preferred collections to put at the top of the list. The collection column of the table is turned into a factor for more useful display with datatable's filter. Specifcying collections here will put those collections at the front of the factor levels and therofre prioritize their display in the select dropdown for the filter
a data.table of the statistics that match the filtering criteria. A 0-row data.table is returned if nothing passes.
sres <- sparrow::exampleSparrowResult()
constructGseaResultTable(sres)
#> collection name active
#> <ord> <char> <lgcl>
#> 1: c2 LOPEZ_MESOTELIOMA_SURVIVAL_TIME_UP TRUE
#> 2: c2 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP TRUE
#> 3: c2 PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP TRUE
#> 4: c2 REACTOME_MRNA_SPLICING_MINOR_PATHWAY TRUE
#> 5: c7 GSE3982_BCELL_VS_TH2_DN TRUE
#> 6: c6 E2F3_UP.V1_UP TRUE
#> 7: c7 GSE13485_CTRL_VS_DAY3_YF17D_VACCINE_PBMC_DN TRUE
#> 8: c2 MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN TRUE
#> 9: c6 TBK1.DN.48HRS_DN TRUE
#> 10: c2 VANTVEER_BREAST_CANCER_ESR1_DN TRUE
#> 11: c6 CAMP_UP.V1_DN TRUE
#> 12: c6 KRAS.600.LUNG.BREAST_UP.V1_DN TRUE
#> 13: c7 GSE22886_IGG_IGA_MEMORY_BCELL_VS_BLOOD_PLASMA_CELL_UP TRUE
#> 14: c6 KRAS.BREAST_UP.V1_DN TRUE
#> 15: c2 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN TRUE
#> 16: c6 KRAS.LUNG.BREAST_UP.V1_DN TRUE
#> 17: c6 ATM_DN.V1_UP TRUE
#> 18: c6 KRAS.LUNG_UP.V1_DN TRUE
#> 19: c2 YAMASHITA_LIVER_CANCER_STEM_CELL_DN TRUE
#> 20: c2 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN TRUE
#> 21: c2 BIOCARTA_AGPCR_PATHWAY TRUE
#> 22: c2 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_UP TRUE
#> 23: c2 BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN TRUE
#> 24: c6 KRAS.50_UP.V1_UP TRUE
#> 25: c2 BURTON_ADIPOGENESIS_PEAK_AT_2HR TRUE
#> 26: c2 HUPER_BREAST_BASAL_VS_LUMINAL_UP TRUE
#> 27: c2 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN TRUE
#> collection name active
#> N n pval padj padj.by.collection n.sig n.neutral
#> <int> <int> <num> <num> <num> <int> <int>
#> 1: 14 14 1.695907e-08 4.296298e-07 1.695907e-07 8 6
#> 2: 151 149 9.516274e-41 7.232368e-39 2.854882e-39 80 69
#> 3: 56 55 1.334978e-10 5.072916e-09 2.002467e-09 18 37
#> 4: 45 42 4.100173e-06 6.232263e-05 2.460104e-05 2 40
#> 5: 200 175 2.850357e-04 3.094673e-03 5.700714e-03 30 145
#> 6: 196 155 3.153970e-02 8.877841e-02 9.111468e-02 21 134
#> 7: 200 191 2.523983e-03 1.370162e-02 1.682655e-02 11 180
#> 8: 172 170 1.297630e-03 1.064454e-02 5.135523e-03 10 160
#> 9: 50 50 2.961713e-02 8.877841e-02 9.111468e-02 7 43
#> 10: 240 233 3.609397e-02 9.707699e-02 7.218795e-02 28 205
#> 11: 200 183 3.055288e-02 8.877841e-02 9.111468e-02 22 161
#> 12: 289 189 2.564978e-02 8.475579e-02 9.111468e-02 23 166
#> 13: 200 176 1.256932e-03 1.064454e-02 1.256932e-02 17 159
#> 14: 145 90 2.487090e-02 8.475579e-02 9.111468e-02 9 81
#> 15: 428 356 1.727021e-03 1.093780e-02 5.181062e-03 63 293
#> 16: 145 96 2.273234e-02 8.226941e-02 9.111468e-02 11 85
#> 17: 146 89 1.567032e-02 6.616355e-02 9.111468e-02 13 76
#> 18: 145 98 2.270691e-02 8.226941e-02 9.111468e-02 13 85
#> 19: 76 47 1.518841e-02 6.616355e-02 3.505018e-02 5 42
#> 20: 50 45 1.540657e-03 1.064454e-02 5.135523e-03 7 38
#> 21: 13 11 2.271767e-02 8.226941e-02 4.868071e-02 1 10
#> 22: 9 9 7.265220e-03 3.681045e-02 1.816305e-02 2 7
#> 23: 51 41 4.310320e-05 5.459739e-04 2.155160e-04 9 32
#> 24: 48 33 1.330857e-02 6.321570e-02 9.111468e-02 10 23
#> 25: 51 50 1.473643e-03 1.064454e-02 5.135523e-03 9 41
#> 26: 54 52 2.162668e-03 1.264329e-02 5.898185e-03 9 43
#> 27: 91 91 2.766197e-06 5.255773e-05 2.074647e-05 20 71
#> N n pval padj padj.by.collection n.sig n.neutral
#> n.up n.down n.sig.up n.sig.down mean.logFC mean.logFC.trim mean.t
#> <int> <int> <int> <int> <num> <num> <num>
#> 1: 14 0 8 0 1.9053048 1.9201957 2.6611296
#> 2: 147 2 80 0 1.8402359 1.8310993 2.8107308
#> 3: 47 8 18 0 1.0281693 0.9533016 1.7020744
#> 4: 35 7 2 0 0.3510180 0.3433814 1.2752435
#> 5: 116 59 20 10 0.3908602 0.3337944 0.6218071
#> 6: 98 57 9 12 0.2605313 0.2896170 0.3003986
#> 7: 130 61 4 7 0.2774772 0.2685242 0.4590224
#> 8: 104 66 6 4 0.1972357 0.1685089 0.5338254
#> 9: 31 19 5 2 0.2699208 0.1658724 0.4860196
#> 10: 135 98 20 8 0.2188470 0.1531049 0.2752792
#> 11: 75 108 2 20 -0.2631505 -0.2306874 -0.6154836
#> 12: 77 112 1 22 -0.3056071 -0.2627638 -0.6498984
#> 13: 57 119 0 17 -0.3241097 -0.2890946 -0.8570488
#> 14: 31 59 0 9 -0.3264680 -0.3098887 -0.7466725
#> 15: 137 219 5 58 -0.3405691 -0.3268273 -0.7889832
#> 16: 36 60 1 10 -0.3470210 -0.3396559 -0.7333986
#> 17: 29 60 1 12 -0.4379007 -0.4117162 -0.7610840
#> 18: 34 64 1 12 -0.4812555 -0.4309138 -0.7247246
#> 19: 16 31 0 5 -0.5284611 -0.4369603 -0.8993549
#> 20: 13 32 0 7 -0.4568979 -0.4711493 -1.1350462
#> 21: 3 8 0 1 -0.4953724 -0.5044566 -1.3726441
#> 22: 2 7 0 2 -0.6026479 -0.6026479 -1.7435775
#> 23: 11 30 0 9 -0.7685127 -0.6500474 -1.5021451
#> 24: 9 24 2 8 -0.5773156 -0.6725080 -0.9812401
#> 25: 14 36 1 8 -0.7654912 -0.7382118 -1.0964370
#> 26: 15 37 1 8 -0.6465576 -0.7566993 -1.0664421
#> 27: 24 67 0 20 -0.9569427 -0.9387142 -1.3803432
#> n.up n.down n.sig.up n.sig.down mean.logFC mean.logFC.trim mean.t
#> mean.t.trim Direction rank
#> <num> <char> <int>
#> 1: 2.7229413 Up 3
#> 2: 2.8715625 Up 1
#> 3: 1.8177360 Up 2
#> 4: 1.2959816 Up 5
#> 5: 0.7146269 Up 7
#> 6: 0.3953663 Up 27
#> 7: 0.5821929 Up 14
#> 8: 0.5781200 Up 9
#> 9: 0.5228263 Up 24
#> 10: 0.2928013 Up 28
#> 11: -0.5800135 Down 25
#> 12: -0.5144962 Down 23
#> 13: -0.7581619 Down 8
#> 14: -0.5891867 Down 22
#> 15: -0.7050304 Down 12
#> 16: -0.6149464 Down 21
#> 17: -0.7435324 Down 18
#> 18: -0.6159783 Down 19
#> 19: -0.8207050 Down 17
#> 20: -1.0681036 Down 11
#> 21: -1.3765614 Down 20
#> 22: -1.7435775 Down 15
#> 23: -1.5212565 Down 6
#> 24: -1.1545970 Down 16
#> 25: -1.1564061 Down 10
#> 26: -1.0481488 Down 13
#> 27: -1.2397314 Down 4
#> mean.t.trim Direction rank