Set significant and number of genes
set_significant_N_genes(
genelist,
significance_by = "pvalue_effectsize",
pvalue_threshold = 0.05,
effectsize_threshold = 1,
keep_max_n_genes = FALSE,
keep_max_n_genes_by = "pvalue"
)list, loaded genelist with goatea::read_validate_genelist()
string, default: 'pvalue_effectsize', else 'pvalue' or 'effectsize' to set gene significance to TRUE/FALSE in 'signif' column
numeric, default: 0.05, to set gene significance based on pvalue
numeric, default: 1, to set gene significance based on effectsize
boolean, default: TRUE, filter down by pvalue to max n genes allowed by goat (max(goat::goat_nulldistributions$N))
string, default: 'pvalue', else 'effectsize', order genes based on lowest pvalues or highest absolute effect sizes
genelist with added 'signif' column with TRUE/FALSE values
set_significant_N_genes(
get(load(system.file("extdata", "example_genelist.rda", package = "goatea")))
)
#> symbol gene pvalue effectsize signif
#> 1 gene_81 18837 5.471520e-06 -4.3 TRUE
#> 2 gene_77 19922 2.608286e-04 2.4 TRUE
#> 3 gene_17 13765 8.416599e-04 -2.2 TRUE
#> 4 gene_31 14822 1.943295e-03 2.5 TRUE
#> 5 gene_38 12392 2.473132e-03 3.3 TRUE
#> 6 gene_96 19338 3.349992e-03 -3.3 TRUE
#> 7 gene_70 17254 3.575055e-03 4.2 TRUE
#> 8 gene_55 12874 3.598888e-03 -1.1 TRUE
#> 9 gene_72 13860 4.419765e-03 -1.1 TRUE
#> 10 gene_82 19040 5.928995e-03 0.3 FALSE
#> 11 gene_89 16292 6.265346e-03 0.6 FALSE
#> 12 gene_86 15947 7.064525e-03 2.2 TRUE
#> 13 gene_94 18968 7.718095e-03 -3.9 TRUE
#> 14 gene_3 18953 1.082897e-02 3.3 TRUE
#> 15 gene_14 17269 1.189872e-02 -2.4 TRUE
#> 16 gene_76 10534 1.208455e-02 4.8 TRUE
#> 17 gene_18 13317 1.288837e-02 1.8 TRUE
#> 18 gene_95 11862 1.323199e-02 -2.1 TRUE
#> 19 gene_69 19501 1.326578e-02 -4.7 TRUE
#> 20 gene_83 13383 1.574589e-02 -1.9 TRUE
#> 21 gene_51 10162 1.867518e-02 -2.9 TRUE
#> 22 gene_68 14654 2.029972e-02 -4.8 TRUE
#> 23 gene_1 16730 2.035625e-02 -0.2 FALSE
#> 24 gene_50 18362 2.061664e-02 -0.3 FALSE
#> 25 gene_91 11558 2.233164e-02 -4.4 TRUE
#> 26 gene_45 18862 2.257831e-02 -0.9 FALSE
#> 27 gene_23 10244 2.264889e-02 -3.3 TRUE
#> 28 gene_28 12997 2.290224e-02 -0.2 FALSE
#> 29 gene_26 19424 2.411721e-02 -1.7 TRUE
#> 30 gene_49 10593 2.579521e-02 -3.5 TRUE
#> 31 gene_84 12088 2.588124e-02 3.7 TRUE
#> 32 gene_92 14555 2.664260e-02 3.4 TRUE
#> 33 gene_36 18297 2.710420e-02 -1.9 TRUE
#> 34 gene_46 15785 3.223701e-02 2.1 TRUE
#> 35 gene_59 14767 3.259735e-02 -0.6 FALSE
#> 36 gene_80 12272 3.440294e-02 0.3 FALSE
#> 37 gene_73 19244 3.440736e-02 3.0 TRUE
#> 38 gene_47 16613 3.609518e-02 1.2 TRUE
#> 39 gene_15 16230 3.759849e-02 -1.4 TRUE
#> 40 gene_58 13126 3.917926e-02 -2.0 TRUE
#> 41 gene_48 15077 3.976684e-02 -2.0 TRUE
#> 42 gene_8 18324 3.980623e-02 -0.8 FALSE
#> 43 gene_9 17464 4.168482e-02 -3.0 TRUE
#> 44 gene_100 17954 4.195725e-02 2.2 TRUE
#> 45 gene_78 15544 4.259890e-02 2.2 TRUE
#> 46 gene_74 11748 4.320323e-02 -0.8 FALSE
#> 47 gene_42 17176 4.455923e-02 -0.2 FALSE
#> 48 gene_19 16034 4.521529e-02 -4.2 TRUE
#> 49 gene_27 10777 4.590041e-02 0.8 FALSE
#> 50 gene_21 15300 4.778884e-02 0.6 FALSE
#> 51 gene_16 10659 5.682229e-02 -2.4 FALSE
#> 52 gene_43 11421 6.259138e-02 2.9 FALSE
#> 53 gene_29 14969 7.830104e-02 -4.9 FALSE
#> 54 gene_41 16436 1.060913e-01 -3.0 FALSE
#> 55 gene_97 14825 1.094756e-01 -4.4 FALSE
#> 56 gene_7 11758 1.251644e-01 0.7 FALSE
#> 57 gene_90 18830 1.694536e-01 -0.9 FALSE
#> 58 gene_87 18554 1.847286e-01 -1.4 FALSE
#> 59 gene_63 11946 1.880133e-01 -0.4 FALSE
#> 60 gene_13 17523 2.011200e-01 4.7 FALSE
#> 61 gene_62 18117 2.103502e-01 -3.2 FALSE
#> 62 gene_39 10470 2.198964e-01 3.7 FALSE
#> 63 gene_66 12067 2.213642e-01 2.9 FALSE
#> 64 gene_60 18372 2.423701e-01 -0.6 FALSE
#> 65 gene_79 10497 2.586512e-01 -1.3 FALSE
#> 66 gene_11 17372 2.814258e-01 1.4 FALSE
#> 67 gene_12 15042 2.818997e-01 4.8 FALSE
#> 68 gene_5 14578 2.952925e-01 -4.3 FALSE
#> 69 gene_57 18378 3.009721e-01 2.0 FALSE
#> 70 gene_65 19908 3.064217e-01 -4.6 FALSE
#> 71 gene_10 11283 3.278389e-01 1.0 FALSE
#> 72 gene_54 19099 4.216015e-01 -4.4 FALSE
#> 73 gene_85 16057 4.343237e-01 1.7 FALSE
#> 74 gene_25 16883 4.440464e-01 -1.7 FALSE
#> 75 gene_71 19051 4.588497e-01 -4.1 FALSE
#> 76 gene_35 15743 4.711346e-01 4.7 FALSE
#> 77 gene_24 15028 4.790531e-01 -4.1 FALSE
#> 78 gene_99 10452 5.002073e-01 4.5 FALSE
#> 79 gene_64 19911 5.390606e-01 1.5 FALSE
#> 80 gene_88 16875 5.583877e-01 -2.3 FALSE
#> 81 gene_4 18586 5.793203e-01 0.4 FALSE
#> 82 gene_33 13741 5.897144e-01 3.1 FALSE
#> 83 gene_61 14779 7.188174e-01 -3.1 FALSE
#> 84 gene_40 16411 7.214974e-01 2.0 FALSE
#> 85 gene_22 11816 7.720894e-01 1.8 FALSE
#> 86 gene_98 12937 7.906323e-01 -4.8 FALSE
#> 87 gene_93 11537 7.991296e-01 0.3 FALSE
#> 88 gene_67 12006 8.029314e-01 3.4 FALSE
#> 89 gene_75 12070 8.452830e-01 -4.9 FALSE
#> 90 gene_20 18738 8.568102e-01 1.2 FALSE
#> 91 gene_6 12680 9.238778e-01 1.9 FALSE
#> 92 gene_30 11678 9.278401e-01 -0.3 FALSE
#> 93 gene_53 19048 9.305928e-01 -2.9 FALSE
#> 94 gene_34 14867 9.330859e-01 -2.3 FALSE
#> 95 gene_32 17438 9.384276e-01 -4.3 FALSE
#> 96 gene_52 16529 9.505959e-01 0.8 FALSE
#> 97 gene_56 14917 9.514949e-01 2.8 FALSE
#> 98 gene_37 10795 9.542250e-01 -1.3 FALSE
#> 99 gene_2 18348 9.589466e-01 -1.1 FALSE
#> 100 gene_44 19156 9.951943e-01 2.6 FALSE