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_77 13971 0.0005761071 1.9 TRUE
#> 2 gene_37 17976 0.0007281853 1.7 TRUE
#> 3 gene_72 14353 0.0019763106 1.3 TRUE
#> 4 gene_62 19047 0.0026180818 1.1 TRUE
#> 5 gene_24 18669 0.0054691315 0.2 FALSE
#> 6 gene_80 10203 0.0056068281 -3.1 TRUE
#> 7 gene_3 18654 0.0057399258 -1.9 TRUE
#> 8 gene_31 13749 0.0059652171 -4.6 TRUE
#> 9 gene_93 11933 0.0070328307 -0.4 FALSE
#> 10 gene_32 11591 0.0091781541 2.1 TRUE
#> 11 gene_16 13820 0.0098611411 1.9 TRUE
#> 12 gene_50 12972 0.0110291413 -2.7 TRUE
#> 13 gene_35 11766 0.0114130165 -3.6 TRUE
#> 14 gene_2 15182 0.0134083821 2.6 TRUE
#> 15 gene_83 12069 0.0147880407 -4.9 TRUE
#> 16 gene_14 17454 0.0151459930 4.8 TRUE
#> 17 gene_18 12577 0.0154045383 3.6 TRUE
#> 18 gene_76 17267 0.0156027339 -0.1 FALSE
#> 19 gene_88 18991 0.0171371438 -2.3 TRUE
#> 20 gene_85 18008 0.0175477143 1.8 TRUE
#> 21 gene_87 16970 0.0177418999 -3.9 TRUE
#> 22 gene_10 10245 0.0185564985 3.6 TRUE
#> 23 gene_11 14167 0.0212549415 2.4 TRUE
#> 24 gene_56 11666 0.0217266041 -0.8 FALSE
#> 25 gene_73 18041 0.0256478642 -0.1 FALSE
#> 26 gene_75 11867 0.0280972908 1.0 TRUE
#> 27 gene_68 12566 0.0301592460 -2.0 TRUE
#> 28 gene_70 13223 0.0314160230 0.0 FALSE
#> 29 gene_15 18773 0.0319263353 -0.2 FALSE
#> 30 gene_42 10425 0.0327860830 -1.9 TRUE
#> 31 gene_61 11943 0.0330343748 -1.2 TRUE
#> 32 gene_47 17289 0.0346179819 -0.6 FALSE
#> 33 gene_84 17210 0.0351033714 4.2 TRUE
#> 34 gene_64 15285 0.0361981355 -0.1 FALSE
#> 35 gene_46 18408 0.0367585684 4.5 TRUE
#> 36 gene_81 11493 0.0374524091 1.1 TRUE
#> 37 gene_29 11811 0.0376296315 -1.8 TRUE
#> 38 gene_78 17297 0.0380002699 -3.2 TRUE
#> 39 gene_89 18764 0.0381417346 -0.3 FALSE
#> 40 gene_22 18233 0.0396144277 -2.0 TRUE
#> 41 gene_17 19030 0.0401735036 3.8 TRUE
#> 42 gene_63 12543 0.0401987046 4.1 TRUE
#> 43 gene_59 10264 0.0410447186 -4.6 TRUE
#> 44 gene_51 18795 0.0435994704 -3.3 TRUE
#> 45 gene_79 16395 0.0447389679 2.0 TRUE
#> 46 gene_5 13477 0.0452187020 -2.5 TRUE
#> 47 gene_36 19754 0.0455379509 0.1 FALSE
#> 48 gene_27 12137 0.0457239992 -4.0 TRUE
#> 49 gene_71 19591 0.0472080140 -1.0 TRUE
#> 50 gene_19 11321 0.0492537063 1.1 TRUE
#> 51 gene_33 16692 0.0500722567 0.1 FALSE
#> 52 gene_60 15627 0.0803200770 -3.6 FALSE
#> 53 gene_43 14141 0.0925912534 3.8 FALSE
#> 54 gene_53 15513 0.0960559933 -2.3 FALSE
#> 55 gene_4 18229 0.1001915652 1.3 FALSE
#> 56 gene_38 11429 0.1107157922 -3.0 FALSE
#> 57 gene_45 11023 0.1225016047 5.0 FALSE
#> 58 gene_69 14841 0.1287529941 3.3 FALSE
#> 59 gene_97 10828 0.1346589871 3.8 FALSE
#> 60 gene_39 14632 0.1450617983 4.3 FALSE
#> 61 gene_55 19963 0.1515757250 4.2 FALSE
#> 62 gene_82 10679 0.1675504107 0.3 FALSE
#> 63 gene_48 10454 0.1954471020 1.3 FALSE
#> 64 gene_25 19004 0.2083527534 -1.5 FALSE
#> 65 gene_86 16145 0.2550312885 1.9 FALSE
#> 66 gene_28 13600 0.3233845084 -1.5 FALSE
#> 67 gene_74 18124 0.3353291241 2.4 FALSE
#> 68 gene_8 16454 0.3499692532 2.3 FALSE
#> 69 gene_23 17882 0.3731017712 3.2 FALSE
#> 70 gene_96 12308 0.3745010077 4.8 FALSE
#> 71 gene_9 12282 0.3801313830 0.3 FALSE
#> 72 gene_100 19139 0.3894702496 4.5 FALSE
#> 73 gene_40 19010 0.3950270824 4.3 FALSE
#> 74 gene_95 14263 0.4087141513 -1.2 FALSE
#> 75 gene_12 12763 0.4351471254 5.0 FALSE
#> 76 gene_34 16847 0.4351858142 5.0 FALSE
#> 77 gene_20 12460 0.4433733128 -1.9 FALSE
#> 78 gene_6 11722 0.4875204958 3.8 FALSE
#> 79 gene_30 11078 0.5001130297 2.2 FALSE
#> 80 gene_1 10333 0.5403093128 2.5 FALSE
#> 81 gene_67 18157 0.5504981769 -4.5 FALSE
#> 82 gene_91 14584 0.5618272607 -0.8 FALSE
#> 83 gene_41 17539 0.5714313253 1.5 FALSE
#> 84 gene_21 11309 0.5737756956 -3.9 FALSE
#> 85 gene_58 10991 0.5743754293 -1.0 FALSE
#> 86 gene_26 12698 0.5953526736 -4.1 FALSE
#> 87 gene_49 19790 0.6056210295 0.9 FALSE
#> 88 gene_66 11027 0.6598133688 1.0 FALSE
#> 89 gene_57 19013 0.6670528062 -4.8 FALSE
#> 90 gene_92 11532 0.6761687007 4.7 FALSE
#> 91 gene_54 11182 0.6915581074 1.4 FALSE
#> 92 gene_44 16473 0.7670898249 -0.5 FALSE
#> 93 gene_98 19388 0.7766925020 -2.2 FALSE
#> 94 gene_94 17779 0.8444629515 -4.3 FALSE
#> 95 gene_52 13287 0.9258234095 -3.1 FALSE
#> 96 gene_7 18906 0.9268065962 0.0 FALSE
#> 97 gene_90 15371 0.9688015921 1.8 FALSE
#> 98 gene_99 10629 0.9714059386 -3.7 FALSE
#> 99 gene_65 15882 0.9806994354 -0.7 FALSE
#> 100 gene_13 19140 0.9933005570 0.7 FALSE