Given a qseaGLM object with one or more contrasts, extract a wide
results table of statistics, adjusted p-values, and (optionally) group means
and per-sample values.
getDMRsData(
qseaSet,
qseaGLM,
sampleNames = NULL,
variable = NULL,
keepData = FALSE,
keepGroupMeans = FALSE,
FDRthres = 0.05,
keepPvals = FALSE,
keepFragmentInfo = FALSE,
direction = "both"
)qseaSet.
Input object used to obtain metadata and counts.
qseaGLM.
Fitted model returned by fitQseaGLM().
character() or NULL.
Sample names to include as per-sample columns.
Default: NULL (chosen automatically when keepData = TRUE, otherwise
per-sample columns are omitted).
character(1) or NULL.
Sample-table column on which contrasts were based (used to compute group
means).
Default: NULL (required if keepGroupMeans = TRUE).
logical(1).
If TRUE, include per-sample values (beta/NRPM etc.) as columns.
Default: FALSE.
logical(1).
If TRUE, include group mean columns for each contrast side (based on
variable).
Default: FALSE.
numeric(1).
False discovery rate threshold used to flag significance.
Default: 0.05.
logical(1).
If TRUE, include raw (unadjusted) p-values in addition to FDR.
Default: FALSE.
logical(1).
If TRUE, include fragment/MAPQ metrics where available.
Default: FALSE.
character(1).
Direction for significance calling, passed to qsea::isSignificant():
one of "up", "down", or "both".
Default: "both".
A tibble with one row per DMR (window) containing:
Per-contrast statistics (e.g., log2FC, deltaBeta, test statistic).
Multiple-testing output (FDR; optionally raw p-values if keepPvals).
Optional group summaries if keepGroupMeans = TRUE.
Optional per-sample columns if keepData = TRUE (for sampleNames).
Optional fragment/MAPQ metrics if keepFragmentInfo = TRUE.
Significant rows are determined using FDRthres and direction via
qsea::isSignificant(). When keepData = TRUE and sampleNames = NULL,
per-sample columns are included for all samples in the fitted model (or the
subset relevant to each contrast, depending on the internal representation).
Group means require variable to identify the groupings used in contrasts.
Other DMR-detection:
calculateDMRs(),
fitQseaGLM(),
makeAllContrasts()
data(exampleTumourNormal, package = "mesa")
qs <- exampleTumourNormal
contr <- tibble::tibble(group1 = "LUAD", group2 = "NormalLung")
glmfit <- fitQseaGLM(qs, variable = "type", contrasts = contr)
#> Generating table of nrpm values for 819 regions across 5 samples.
#> Fitting initial GLM on 255 windows, without using parallelisation.
#> Performing contrast LUAD_vs_NormalLung
#> Contrasts Complete
getDMRsData(qs, glmfit, variable = "type", FDRthres = 0.1)
#> selecting regions from contrast LUAD_vs_NormalLung
#> selected 58/255 windows
#> adding test results from LUAD_vs_NormalLung
#> chr window_start window_end CpG_density LUAD_vs_NormalLung_log2FC
#> 1 7 25107301 25107600 8.129562 -1.7065113
#> 2 7 27096001 27096300 18.819360 3.7189840
#> 3 7 27096301 27096600 19.869991 3.3847190
#> 4 7 27096601 27096900 12.621572 2.4383303
#> 5 7 27096901 27097200 17.859145 2.9924262
#> 6 7 27098401 27098700 12.091314 1.1149731
#> 7 7 27099001 27099300 13.110241 0.8566084
#> 8 7 27103501 27103800 13.065380 1.7221760
#> 9 7 27106501 27106800 18.975041 1.0607944
#> 10 7 27106801 27107100 13.121566 1.3817939
#> 11 7 27108301 27108600 15.663462 1.0579513
#> 12 7 27108601 27108900 16.137669 0.9743731
#> 13 7 27113401 27113700 16.196189 1.0095730
#> 14 7 27113701 27114000 20.416269 0.7745009
#> 15 7 27124201 27124500 18.103046 1.1060122
#> 16 7 27129901 27130200 15.153912 0.9682945
#> 17 7 27130201 27130500 28.165752 1.0704286
#> 18 7 27130501 27130800 21.505199 1.2958221
#> 19 7 27130801 27131100 19.733660 0.9878071
#> 20 7 27139501 27139800 20.879425 0.5585066
#> 21 7 27142501 27142800 11.395603 1.1687403
#> 22 7 27144601 27144900 11.126804 1.4418483
#> 23 7 27144901 27145200 16.289011 1.2812704
#> 24 7 27151201 27151500 16.547893 2.3711682
#> 25 7 27156001 27156300 24.495967 2.8051771
#> 26 7 27156301 27156600 18.493412 3.2840309
#> 27 7 27156601 27156900 19.399213 2.6264119
#> 28 7 27164701 27165000 13.844064 1.9860442
#> 29 7 27165301 27165600 21.163787 2.5736742
#> 30 7 27165901 27166200 13.562021 2.5341204
#> 31 7 27166201 27166500 19.991182 3.1848355
#> 32 7 27169801 27170100 18.338350 2.3103492
#> 33 7 27173401 27173700 30.900096 2.7063989
#> 34 7 27174001 27174300 25.134593 3.7351692
#> 35 7 27184801 27185100 15.569914 1.7353119
#> 36 7 27185701 27186000 12.453860 2.7893369
#> 37 7 27191701 27192000 6.785994 1.9947983
#> 38 7 27192301 27192600 13.204683 1.9402505
#> 39 7 27199201 27199500 19.364907 3.8612649
#> 40 7 27199501 27199800 34.796289 3.7792822
#> 41 7 27199801 27200100 28.271296 2.5713934
#> 42 7 27200101 27200400 30.300691 2.4545847
#> 43 7 27204901 27205200 16.907609 2.9896738
#> 44 7 27205201 27205500 18.542865 2.9694902
#> 45 7 27205501 27205800 13.388085 2.4793682
#> 46 7 27213601 27213900 13.029319 1.9729611
#> 47 7 27239101 27239400 10.828802 2.7070290
#> 48 7 27242401 27242700 11.744126 2.0136327
#> 49 7 27242701 27243000 16.860626 2.2424681
#> 50 7 27243001 27243300 18.365045 2.2384077
#> 51 7 27245101 27245400 17.281498 3.2309411
#> 52 7 27246001 27246300 29.640736 3.1687693
#> 53 7 27246301 27246600 18.853173 2.4288265
#> 54 7 27251401 27251700 18.043771 2.3570533
#> 55 7 27251701 27252000 18.786051 3.1453415
#> 56 7 27252301 27252600 14.980169 1.6412694
#> 57 7 27507901 27508200 11.079548 -1.0032131
#> 58 7 27868201 27868500 7.998633 1.0103877
#> LUAD_vs_NormalLung_adjPval NormalColon_beta_means CRC_beta_means
#> 1 4.249046e-02 0.36370285 0.29310551
#> 2 1.003167e-05 0.02286389 0.02588171
#> 3 9.897733e-07 0.04307951 0.01325373
#> 4 4.445682e-02 0.03170254 0.01868625
#> 5 4.473559e-02 0.03411764 0.01357622
#> 6 5.498550e-03 0.20297172 0.48436703
#> 7 7.828511e-02 0.30363451 0.48698708
#> 8 3.659989e-03 0.24697270 0.68648415
#> 9 2.717567e-07 0.97201574 0.98292081
#> 10 4.473559e-02 0.85935983 0.95764877
#> 11 1.995176e-03 0.32507602 0.70224505
#> 12 1.152404e-05 0.89503296 0.98057606
#> 13 2.230681e-02 0.78444830 0.82435567
#> 14 6.579928e-02 0.52210043 0.60037743
#> 15 1.251189e-03 0.80256807 0.94942989
#> 16 4.775275e-02 0.13286325 0.13035800
#> 17 1.929059e-03 0.17113585 0.15290244
#> 18 3.659989e-03 0.17221249 0.08266116
#> 19 5.437887e-03 0.12017964 0.11589162
#> 20 7.828511e-02 0.65816630 0.62165157
#> 21 6.579928e-02 0.25625255 0.43063974
#> 22 1.188905e-02 0.47603677 0.78244803
#> 23 1.163464e-02 0.42298202 0.66203729
#> 24 4.249046e-02 0.03506450 0.01396020
#> 25 6.529381e-03 0.04213108 0.03699862
#> 26 1.102835e-04 0.02295578 0.01889398
#> 27 2.040101e-02 0.04335333 0.01929138
#> 28 5.437887e-03 0.03911652 0.10380498
#> 29 1.275336e-03 0.08651450 0.08482129
#> 30 3.995843e-02 0.02807925 0.03109415
#> 31 6.826916e-05 0.06829925 0.04383712
#> 32 4.994328e-02 0.04379576 0.02499268
#> 33 9.502693e-02 0.03136274 0.01858256
#> 34 2.244362e-03 0.03162274 0.04360216
#> 35 6.077270e-02 0.03519309 0.02093792
#> 36 8.894003e-03 0.10932018 0.23565668
#> 37 6.579928e-02 0.29353858 0.66436957
#> 38 2.040101e-02 0.11183070 0.26083054
#> 39 2.723638e-07 0.05432257 0.22507125
#> 40 7.482190e-06 0.02185572 0.18487265
#> 41 1.477529e-02 0.02197349 0.02483436
#> 42 8.085397e-02 0.03228571 0.01859282
#> 43 1.102835e-04 0.04687426 0.32879281
#> 44 3.659989e-03 0.02294116 0.31977962
#> 45 2.230681e-02 0.04212668 0.11388968
#> 46 5.437887e-03 0.40529413 0.45502346
#> 47 7.279364e-02 0.23813686 0.43456669
#> 48 4.994328e-02 0.03755351 0.31951249
#> 49 6.529381e-03 0.02362522 0.19523697
#> 50 9.980054e-02 0.06582101 0.31364702
#> 51 9.717466e-06 0.52197319 0.77287623
#> 52 6.529381e-03 0.19122533 0.24147975
#> 53 9.221186e-03 0.25464207 0.56599921
#> 54 2.239728e-02 0.54631149 0.76946917
#> 55 3.659989e-03 0.52886685 0.79163784
#> 56 6.365457e-02 0.23008218 0.47327538
#> 57 1.998963e-02 0.69704437 0.78735613
#> 58 5.984919e-02 0.61821816 0.79330176
#> NormalLung_beta_means LUAD_beta_means LUSC_beta_means NormalColon_nrpm_means
#> 1 0.73101186 0.2834120 0.37480694 0.5084767
#> 2 0.01417545 0.1677325 0.01314872 0.0000000
#> 3 0.02059205 0.2348305 0.01300140 0.2542384
#> 4 0.02820954 0.1314124 0.01876518 0.0000000
#> 5 0.02564357 0.2112698 0.02459035 0.1313856
#> 6 0.30027544 0.6306922 0.18304233 1.2541261
#> 7 0.33541583 0.6099160 0.55375721 2.3853995
#> 8 0.13858124 0.4539004 0.84722430 1.8854556
#> 9 0.68344021 0.9612808 0.98247177 20.3253965
#> 10 0.42786408 0.9046260 0.95249347 8.5843745
#> 11 0.28559086 0.5758667 0.66329401 3.1481146
#> 12 0.59259935 0.9286236 0.96879647 11.1267582
#> 13 0.57302645 0.9209585 0.65024220 8.9444000
#> 14 0.39199634 0.6752420 0.51528249 5.6734326
#> 15 0.40300827 0.8333684 0.88593261 9.0041299
#> 16 0.16572093 0.3335567 0.15707347 1.1227405
#> 17 0.26332425 0.5847100 0.23708342 1.7540700
#> 18 0.17852187 0.4516687 0.19034667 1.7199386
#> 19 0.25798018 0.5234269 0.34906608 1.1227405
#> 20 0.60809558 0.8399465 0.96660709 7.7704623
#> 21 0.35330371 0.7546987 0.53534250 1.3684460
#> 22 0.36405414 0.8525419 0.93074734 2.5338508
#> 23 0.30045638 0.7203546 0.92461431 4.2623223
#> 24 0.03379956 0.1656241 0.58837300 0.1313856
#> 25 0.03130510 0.2097657 0.35308027 0.2542384
#> 26 0.01732460 0.1637919 0.20884704 0.0000000
#> 27 0.03350863 0.2112362 0.29798511 0.2457055
#> 28 0.05272678 0.2255858 0.52437717 0.1228528
#> 29 0.06349829 0.3826259 0.85650855 0.7541823
#> 30 0.04419892 0.2567779 0.26027444 0.0000000
#> 31 0.04371204 0.4043887 0.88285598 0.5255424
#> 32 0.03725410 0.1906839 0.15637345 0.2542384
#> 33 0.01706855 0.1190691 0.03538935 0.1228528
#> 34 0.02866833 0.4126316 0.02336244 0.1228528
#> 35 0.03820756 0.1212005 0.02624241 0.1228528
#> 36 0.03447713 0.2216658 0.67096195 0.6142638
#> 37 0.34993766 0.7881975 0.83614153 0.1313856
#> 38 0.04504492 0.1665715 0.13431037 0.7456494
#> 39 0.02206333 0.3376115 0.02408731 0.3685583
#> 40 0.02169769 0.2867515 0.02309541 0.0000000
#> 41 0.02006125 0.1178889 0.03549393 0.0000000
#> 42 0.02651153 0.1398045 0.02317175 0.1313856
#> 43 0.03543559 0.2937723 0.32410728 0.2627712
#> 44 0.03886381 0.3253825 0.51223154 0.0000000
#> 45 0.02284725 0.1176049 0.14803003 0.1313856
#> 46 0.05811173 0.2301713 0.31363480 3.2419759
#> 47 0.03822530 0.2484144 0.11047895 1.0340192
#> 48 0.04208650 0.1706362 0.48999286 0.0000000
#> 49 0.02923750 0.1449000 0.37899873 0.0000000
#> 50 0.03910405 0.1861609 0.24892524 0.4999439
#> 51 0.03161635 0.2928641 0.18636874 8.1203091
#> 52 0.02178503 0.1885801 0.04798069 1.9707841
#> 53 0.02526573 0.1351582 0.02422962 2.6021136
#> 54 0.03850327 0.1994017 0.70132732 7.5691681
#> 55 0.03006800 0.2716173 0.66809579 10.0910932
#> 56 0.03838645 0.1161913 0.20257960 2.0851040
#> 57 0.87876363 0.4836175 0.58430132 3.9449611
#> 58 0.69559320 0.8854112 0.60287717 1.1398062
#> CRC_nrpm_means NormalLung_nrpm_means LUAD_nrpm_means LUSC_nrpm_means
#> 1 0.43992120 1.41798873 0.2840043 0.5385992
#> 2 0.17836794 0.00000000 1.6630471 0.0000000
#> 3 0.00000000 0.07623409 2.2237345 0.0000000
#> 4 0.00000000 0.07102760 0.8886193 0.0000000
#> 5 0.00000000 0.12113629 2.3818535 0.1346498
#> 6 3.25761743 1.88408527 3.9716880 1.0771984
#> 7 3.81051826 2.49134539 4.4328264 4.1741437
#> 8 5.96293082 1.00107859 3.1752964 6.7324899
#> 9 24.58199741 7.12035324 14.2090623 17.3698239
#> 10 13.61976028 3.12463796 8.8393165 9.6947854
#> 11 7.54404876 2.65455474 5.4429584 6.1938907
#> 12 19.14876854 5.78380509 10.9342169 13.1956802
#> 13 9.14356050 5.46226470 10.6692278 6.1938907
#> 14 6.65240799 3.96464930 6.7634311 5.2513421
#> 15 15.27846276 3.96646321 8.7178037 9.4254858
#> 16 1.18898698 1.44411413 2.7917431 1.3464980
#> 17 1.65270383 2.74120181 5.7679416 2.4236964
#> 18 0.86204540 1.73988798 4.4401477 1.8850972
#> 19 1.30796524 2.61328036 5.2292180 3.5008947
#> 20 6.91976098 6.33360793 9.1086783 13.5996295
#> 21 2.50875059 1.81249424 4.1488221 2.8276457
#> 22 6.34306450 1.70855609 4.9305712 6.1938907
#> 23 8.50687757 2.80803815 6.9844927 10.0987348
#> 24 0.00000000 0.21828929 1.6776896 5.6552915
#> 25 0.28534892 0.22168186 2.3672109 3.6355445
#> 26 0.06538832 0.03811704 1.6703683 2.0197470
#> 27 0.08918397 0.22688835 2.3745322 2.9622955
#> 28 0.71927148 0.31330018 1.6337620 4.3087935
#> 29 0.74306713 0.54018853 4.3289049 9.1561862
#> 30 0.13077663 0.23367351 2.2749833 2.0197470
#> 31 0.39832854 0.31669276 4.2996198 9.5601356
#> 32 0.15457229 0.23888000 2.0758854 1.4811478
#> 33 0.08918397 0.04150962 0.8373705 0.2692996
#> 34 0.35073723 0.16264591 3.4856371 0.1346498
#> 35 0.08918397 0.23367351 1.0803959 0.1346498
#> 36 1.95604868 0.11253722 1.5781406 4.5780931
#> 37 1.26637258 0.29610204 1.4639492 1.3464980
#> 38 2.51494816 0.23028093 1.2794938 0.9425486
#> 39 2.89547969 0.08301925 3.0684262 0.1346498
#> 40 2.47335549 0.10914464 3.2411877 0.1346498
#> 41 0.17836794 0.07962667 1.2868150 0.2692996
#> 42 0.08918397 0.15404684 1.5854619 0.1346498
#> 43 4.12025961 0.20415554 2.8210281 3.0969453
#> 44 4.07266830 0.24566516 2.8693283 5.1166923
#> 45 1.02261633 0.04150962 0.8886193 1.0771984
#> 46 3.79292018 0.31330018 1.6557258 2.2890466
#> 47 2.03303644 0.03811704 1.1945874 0.4039494
#> 48 2.40796718 0.11774371 0.9881682 2.8276457
#> 49 2.40796718 0.15586076 1.3717215 3.6355445
#> 50 4.00727998 0.27179056 2.0832066 2.4236964
#> 51 9.65447081 0.19216389 3.0420898 1.7504474
#> 52 2.33618237 0.10914464 2.1754343 0.4039494
#> 53 7.21670933 0.12113629 1.3790427 0.1346498
#> 54 9.78524744 0.26839798 2.1754343 7.0017895
#> 55 13.10225455 0.18877131 3.0640536 6.7324899
#> 56 4.69655824 0.23028093 0.9808470 1.7504474
#> 57 4.75014819 5.18458061 2.4447961 2.8276457
#> 58 1.80727612 1.27072704 2.7068367 0.9425486