Generate a tidy table with the results of DESeq
deseqresult2tbl(deseqresult)A DESeq2::DESeqResults() object
A "tidy" data.frame with all genes
# with simulated data...
library(DESeq2)
dds <- DESeq2::makeExampleDESeqDataSet(n = 100, m = 8, betaSD = 1)
dds <- DESeq2::DESeq(dds)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
res <- DESeq2::results(dds)
deseqresult2tbl(res)
#> Warning: Please use `mosdef::deresult_to_df()` in replacement of the `deseqresult2tbl()` function, originally located in the ideal package.
#> Check the manual page for `?mosdef::deresult_to_df()` to see the details on how to use it, e.g. refer to the new parameter definition and naming
#> id baseMean log2FoldChange lfcSE stat pvalue
#> gene18 gene18 147.7672115 1.81180737 0.3686343 4.91491833 8.881948e-07
#> gene60 gene60 46.2117002 -2.30736434 0.4869602 -4.73830204 2.155164e-06
#> gene49 gene49 158.0878830 -1.77872348 0.4018392 -4.42645570 9.579405e-06
#> gene53 gene53 56.4539309 2.14780789 0.4837266 4.44012781 8.990547e-06
#> gene4 gene4 11.7942965 4.55988006 1.1262978 4.04855647 5.153450e-05
#> gene37 gene37 176.3726912 -1.67093529 0.4226210 -3.95374438 7.693760e-05
#> gene92 gene92 175.9733980 1.54740357 0.4007370 3.86139464 1.127416e-04
#> gene36 gene36 92.8407969 1.93239884 0.5048087 3.82798263 1.291979e-04
#> gene48 gene48 30.4723121 2.34723328 0.6916218 3.39381066 6.892733e-04
#> gene46 gene46 8.5793311 -2.77782874 0.9074062 -3.06128469 2.203894e-03
#> gene21 gene21 24.8595855 1.56326481 0.5231209 2.98834303 2.804945e-03
#> gene15 gene15 9.5788500 2.21770592 0.8080480 2.74452250 6.059900e-03
#> gene8 gene8 16.5528205 -1.67399665 0.6457407 -2.59236652 9.531816e-03
#> gene54 gene54 6.0058185 -2.51750607 1.0180315 -2.47291581 1.340157e-02
#> gene30 gene30 43.4305173 1.34138186 0.5800370 2.31257990 2.074575e-02
#> gene42 gene42 55.0885987 1.08580918 0.4770517 2.27608278 2.284106e-02
#> gene43 gene43 12.9858958 -1.49771300 0.6545149 -2.28827934 2.212126e-02
#> gene75 gene75 116.1426810 1.22606727 0.5432433 2.25693937 2.401186e-02
#> gene79 gene79 47.6292374 -1.09029621 0.4769335 -2.28605506 2.225104e-02
#> gene85 gene85 33.0411647 -1.02506194 0.4367920 -2.34679668 1.893558e-02
#> gene81 gene81 24.0312805 -1.48459644 0.6713788 -2.21126493 2.701750e-02
#> gene29 gene29 63.0771671 -1.07928627 0.5376468 -2.00742607 4.470432e-02
#> gene40 gene40 9.5288356 1.88458618 0.9792124 1.92459391 5.428018e-02
#> gene66 gene66 16.3941665 -1.15943246 0.6083937 -1.90572715 5.668562e-02
#> gene26 gene26 15.8285239 -1.38367754 0.7668934 -1.80426328 7.119004e-02
#> gene16 gene16 32.1330846 -0.76434535 0.4382109 -1.74424098 8.111708e-02
#> gene71 gene71 12.7817906 1.36388808 0.7851506 1.73710370 8.236887e-02
#> gene5 gene5 6.0124241 -1.81829129 1.1130781 -1.63357032 1.023491e-01
#> gene13 gene13 6.4063855 -1.49460009 0.9147094 -1.63396170 1.022669e-01
#> gene23 gene23 13.4648587 1.21480571 0.7114228 1.70757212 8.771577e-02
#> gene31 gene31 24.5704309 1.25738995 0.7636200 1.64661746 9.963670e-02
#> gene62 gene62 5.1692910 -2.12569227 1.2953884 -1.64096904 1.008038e-01
#> gene95 gene95 21.4640620 0.87067439 0.5231249 1.66437202 9.603811e-02
#> gene86 gene86 221.9549512 0.55484371 0.3529658 1.57194767 1.159627e-01
#> gene35 gene35 26.4328448 -0.68474822 0.4983452 -1.37404403 1.694280e-01
#> gene65 gene65 32.4237187 -0.75311719 0.5684238 -1.32492197 1.851970e-01
#> gene96 gene96 30.6283666 0.76853965 0.5997525 1.28142795 2.000434e-01
#> gene3 gene3 5.2306502 -1.11346675 0.9780366 -1.13847140 2.549237e-01
#> gene11 gene11 6.4005978 1.06668978 0.9803392 1.08808233 2.765588e-01
#> gene17 gene17 1391.8628616 0.37605638 0.3382549 1.11175445 2.662437e-01
#> gene70 gene70 6.6501426 0.92780707 0.8680806 1.06880293 2.851585e-01
#> gene89 gene89 36.6558955 -0.57596358 0.5403255 -1.06595672 2.864432e-01
#> gene67 gene67 27.9234651 -0.53718367 0.5176427 -1.03774985 2.993865e-01
#> gene12 gene12 90.2425723 -0.43366393 0.4371815 -0.99195399 3.212200e-01
#> gene47 gene47 20.3033965 0.74597537 0.7629593 0.97773943 3.282032e-01
#> gene51 gene51 56.4652546 0.44687893 0.4635993 0.96393350 3.350793e-01
#> gene56 gene56 94.4751277 0.37403462 0.3851316 0.97118661 3.314554e-01
#> gene69 gene69 59.7861354 0.44439149 0.4564299 0.97362491 3.302428e-01
#> gene100 gene100 19.9579969 0.68554977 0.7297941 0.93937427 3.475386e-01
#> gene80 gene80 31.0274383 -0.50935446 0.5708139 -0.89233023 3.722160e-01
#> gene39 gene39 11.3378252 -0.58412561 0.7063621 -0.82694923 4.082658e-01
#> gene7 gene7 21.7636045 0.43516949 0.5566033 0.78183063 4.343141e-01
#> gene45 gene45 14.7497426 -0.58419746 0.7227839 -0.80826018 4.189408e-01
#> gene61 gene61 20.1452134 -0.46556041 0.5944918 -0.78312333 4.335547e-01
#> gene63 gene63 14.9836946 -0.50678268 0.6713637 -0.75485561 4.503356e-01
#> gene33 gene33 19.5336530 -0.41848060 0.5806479 -0.72071319 4.710860e-01
#> gene88 gene88 52.1231411 -0.33328987 0.4546401 -0.73308512 4.635065e-01
#> gene41 gene41 6.3492340 -0.61221774 0.9174292 -0.66731876 5.045685e-01
#> gene59 gene59 13.1651336 0.64283316 0.9564520 0.67210186 5.015189e-01
#> gene87 gene87 4.4440153 0.67929922 0.9713311 0.69934881 4.843341e-01
#> gene99 gene99 275.6150416 -0.29462152 0.4295066 -0.68595335 4.927425e-01
#> gene1 gene1 3.8392185 0.67384885 1.2030111 0.56013519 5.753872e-01
#> gene10 gene10 6.5887951 0.62179064 1.0837341 0.57374832 5.661381e-01
#> gene57 gene57 6.8034194 -0.48962702 0.8833023 -0.55431422 5.793638e-01
#> gene93 gene93 18.8449121 0.34888736 0.6464980 0.53965731 5.894334e-01
#> gene27 gene27 4.9642290 -0.65003837 1.3018191 -0.49933079 6.175464e-01
#> gene78 gene78 9.6375469 0.45507594 0.8673976 0.52464514 5.998299e-01
#> gene90 gene90 22.9211061 0.32104338 0.6281354 0.51110540 6.092773e-01
#> gene77 gene77 5.4123345 0.43505735 0.9837035 0.44226474 6.582976e-01
#> gene58 gene58 68.3003757 0.16705903 0.4459982 0.37457331 7.079778e-01
#> gene52 gene52 11.3296541 0.31599323 0.8812153 0.35858801 7.199033e-01
#> gene44 gene44 63.0369191 0.13387207 0.4195890 0.31905522 7.496846e-01
#> gene94 gene94 86.0570634 0.12124901 0.3763524 0.32216880 7.473248e-01
#> gene25 gene25 31.6298448 -0.13956872 0.5122069 -0.27248506 7.852491e-01
#> gene55 gene55 12.8749623 -0.18290707 0.6649339 -0.27507558 7.832582e-01
#> gene76 gene76 59.9514264 -0.14486450 0.4937379 -0.29340363 7.692136e-01
#> gene72 gene72 32.7347702 0.13428254 0.5482607 0.24492460 8.065148e-01
#> gene9 gene9 7.2478328 -0.16791632 0.8979562 -0.18699833 8.516619e-01
#> gene20 gene20 127.6055875 -0.07480987 0.3854973 -0.19406071 8.461283e-01
#> gene22 gene22 26.8980437 -0.10288668 0.5614556 -0.18324987 8.546020e-01
#> gene32 gene32 41.7556954 -0.04366768 0.4501030 -0.09701707 9.227128e-01
#> gene83 gene83 7.4533000 0.02898913 0.9773727 0.02966026 9.763380e-01
#> gene2 gene2 1.4282806 -2.41236030 1.8007965 -1.33960741 1.803730e-01
#> gene6 gene6 0.0000000 NA NA NA NA
#> gene14 gene14 2.6542864 0.29120929 1.4432203 0.20177743 8.400907e-01
#> gene19 gene19 1.0868084 3.60628939 2.6374248 1.36735250 1.715148e-01
#> gene24 gene24 1.6695261 0.34604530 1.6676830 0.20750065 8.356189e-01
#> gene28 gene28 1.8363302 -1.97980220 1.9197535 -1.03127936 3.024098e-01
#> gene34 gene34 1.2689141 -0.32804349 1.9576886 -0.16756674 8.669241e-01
#> gene38 gene38 0.2383993 -1.48142894 3.5322017 -0.41940666 6.749190e-01
#> gene50 gene50 0.2383993 -1.48142894 3.5322017 -0.41940666 6.749190e-01
#> gene64 gene64 3.6161705 -1.73328483 1.6008438 -1.08273203 2.789274e-01
#> gene68 gene68 1.0560216 -3.61265286 2.9826735 -1.21121299 2.258138e-01
#> gene73 gene73 5.8940837 -1.12781617 1.3617290 -0.82822367 NA
#> gene74 gene74 2.2734338 -2.44088593 1.8927070 -1.28962697 1.971802e-01
#> gene82 gene82 1.9571366 1.15281811 1.6087710 0.71658311 4.736314e-01
#> gene84 gene84 0.8252266 -2.34184359 2.2461682 -1.04259495 2.971359e-01
#> gene91 gene91 3.0676579 -2.13899624 1.3472277 -1.58770210 1.123537e-01
#> gene97 gene97 2.1419029 -1.41655534 1.4225627 -0.99577706 3.193585e-01
#> gene98 gene98 3.5736711 0.86849726 1.4523690 0.59798663 5.498489e-01
#> padj
#> gene18 7.283197e-05
#> gene60 8.836173e-05
#> gene49 1.963778e-04
#> gene53 1.963778e-04
#> gene4 8.451658e-04
#> gene37 1.051481e-03
#> gene92 1.320688e-03
#> gene36 1.324278e-03
#> gene48 6.280046e-03
#> gene46 1.807193e-02
#> gene21 2.090959e-02
#> gene15 4.140932e-02
#> gene8 6.012376e-02
#> gene54 7.849492e-02
#> gene30 9.844864e-02
#> gene42 9.844864e-02
#> gene43 9.844864e-02
#> gene75 9.844864e-02
#> gene79 9.844864e-02
#> gene85 9.844864e-02
#> gene81 1.054969e-01
#> gene29 1.666252e-01
#> gene40 1.935206e-01
#> gene66 1.936759e-01
#> gene26 2.335033e-01
#> gene16 2.501573e-01
#> gene71 2.501573e-01
#> gene5 2.543220e-01
#> gene13 2.543220e-01
#> gene23 2.543220e-01
#> gene31 2.543220e-01
#> gene62 2.543220e-01
#> gene95 2.543220e-01
#> gene86 2.796747e-01
#> gene35 3.969456e-01
#> gene65 4.218377e-01
#> gene96 4.433394e-01
#> gene3 5.500985e-01
#> gene11 5.592463e-01
#> gene17 5.592463e-01
#> gene70 5.592463e-01
#> gene89 5.592463e-01
#> gene67 5.709232e-01
#> gene12 5.724271e-01
#> gene47 5.724271e-01
#> gene51 5.724271e-01
#> gene56 5.724271e-01
#> gene69 5.724271e-01
#> gene100 5.815952e-01
#> gene80 6.104342e-01
#> gene39 6.564274e-01
#> gene7 6.595140e-01
#> gene45 6.595140e-01
#> gene61 6.595140e-01
#> gene63 6.714095e-01
#> gene33 6.777027e-01
#> gene88 6.777027e-01
#> gene41 6.782725e-01
#> gene59 6.782725e-01
#> gene87 6.782725e-01
#> gene99 6.782725e-01
#> gene1 7.423099e-01
#> gene10 7.423099e-01
#> gene57 7.423099e-01
#> gene93 7.435929e-01
#> gene27 7.446883e-01
#> gene78 7.446883e-01
#> gene90 7.446883e-01
#> gene77 7.823247e-01
#> gene58 8.293455e-01
#> gene52 8.314376e-01
#> gene44 8.421115e-01
#> gene94 8.421115e-01
#> gene25 8.472424e-01
#> gene55 8.472424e-01
#> gene76 8.472424e-01
#> gene72 8.588859e-01
#> gene9 8.759670e-01
#> gene20 8.759670e-01
#> gene22 8.759670e-01
#> gene32 9.341044e-01
#> gene83 9.763380e-01
#> gene2 NA
#> gene6 NA
#> gene14 NA
#> gene19 NA
#> gene24 NA
#> gene28 NA
#> gene34 NA
#> gene38 NA
#> gene50 NA
#> gene64 NA
#> gene68 NA
#> gene73 NA
#> gene74 NA
#> gene82 NA
#> gene84 NA
#> gene91 NA
#> gene97 NA
#> gene98 NA