A wrapper function used to perform qSVA in one step.
qSVA(rse_tx, sig_transcripts = select_transcripts(), mod, assayname)A RangedSummarizedExperiment-class object containing the transcript data desired to be studied.
A character() vector of transcripts that should be
associated with degradation, expected to be present in rownames(rse_tx).
Model Matrix with necessary variables the you would model for in differential expression.
character string specifying the name of the assay desired in rse_tx
matrix with k principal components for each sample
## First we need to define a statistical model. We'll use the example
## rse_tx data. Note that the model you'll use in your own data
## might look different from this model.
mod <- model.matrix(~ mitoRate + Region + rRNA_rate + totalAssignedGene + RIN,
data = colData(rse_tx)
)
## To ensure that the results are reproducible, you will need to set a
## random seed with the set.seed() function. Internally, we are using
## sva::num.sv() which needs a random seed to ensure reproducibility of the
## results.
set.seed(20230621)
qSVA(rse_tx = rse_tx, mod = mod, assayname = "tpm")
#> Using 1044 degradation-associated transcripts.
#> qSV1 qSV2 qSV3 qSV4 qSV5
#> DLPFC_Br1385_A1_ribo -15.8672721 -12.3706539 -1.8250557 1.51888632 -0.01218481
#> DLPFC_Br1385_A2_ribo 1.6556199 -8.0281324 -1.0738816 -4.50675618 -8.58825752
#> DLPFC_Br1385_A3_ribo 25.3384820 -5.3240146 3.3150845 -0.56546246 -1.79096470
#> DLPFC_Br1385_A4_ribo 15.5859442 -10.4722056 0.3932367 0.99627839 -4.19047380
#> DLPFC_Br1729_B1_ribo -19.0007397 -12.2808055 -3.2636667 2.36908526 3.22374567
#> DLPFC_Br1729_B2_ribo -11.6801225 -11.4216642 -3.5355365 2.59402359 -0.14089959
#> DLPFC_Br1729_B3_ribo 33.5338036 -9.4991199 0.9506116 -4.88265288 2.67239443
#> DLPFC_Br1729_B4_ribo 6.7616423 -11.3475373 -2.7645155 6.56305015 2.40399963
#> DLPFC_Br2015_F1_ribo -21.6646587 -4.4813660 -2.5604991 -6.62907017 -4.29788099
#> DLPFC_Br2015_F2_ribo -6.0196725 -8.5483118 -2.5461525 1.48356212 -0.10765696
#> DLPFC_Br2015_F3_ribo 14.0693876 -4.1953416 3.2272074 -0.43368309 1.44563204
#> DLPFC_Br2015_F4_ribo 9.0662610 -11.3620345 -2.3466733 -5.51689536 3.43711249
#> DLPFC_Br2020_C1_ribo -17.7970001 -10.4456548 -4.0617924 1.65550803 -0.31407413
#> DLPFC_Br2020_C2_ribo 2.7134773 -12.7331262 -4.4315213 5.48231731 -2.32052637
#> DLPFC_Br2020_C3_ribo 41.3621779 -10.0975048 2.4201913 -6.52387331 3.65186231
#> DLPFC_Br2020_C4_ribo 19.4249036 -11.1049686 -2.0921942 4.64493744 -1.46323248
#> DLPFC_Br2074_D1_ribo -31.3822759 -4.2196405 -1.6018474 -7.56412052 -7.23769162
#> DLPFC_Br2074_D2_ribo -14.6788526 -12.3946647 -3.9470495 1.68872681 -1.18334265
#> DLPFC_Br2074_D3_ribo 22.2372531 -17.5881834 -0.4283349 -9.31245868 3.92253931
#> DLPFC_Br2074_D4_ribo -6.6602334 -11.9102376 -2.9932042 1.94225622 -2.97647765
#> Br2623-H1a -17.4368272 3.3103737 8.4901488 -2.23516849 0.09691782
#> Br2623-H1b -8.1086581 3.6500902 5.9787834 -0.62422784 -0.14121237
#> Br2623-H1c -7.9022620 1.9855486 7.4230501 1.25420734 0.47473428
#> Br2623-H1d 6.0361201 5.1841577 9.9366248 0.09940832 -0.18942747
#> Br5005-H2a -25.6966081 -3.3646831 5.4395129 -1.11580169 2.01702683
#> Br5005-H2b -7.0497022 -0.7393247 0.1819131 3.19412165 1.31282809
#> Br5005-H2c -12.3931268 -0.2302357 3.3274929 2.08726661 2.33580293
#> Br5005-H2d -3.3015962 2.0176566 5.6557587 1.88070719 2.50506599
#> Br5370-H3a -15.3021782 -0.1408422 7.7460122 0.45830226 1.31590218
#> Br5370-H3b -0.8750812 0.5281671 3.8815361 3.67581441 -0.34284862
#> Br5370-H3c 0.5837811 1.3426739 7.1195996 3.55593853 0.52337138
#> Br5370-H3d 13.4756531 4.0693719 8.8956802 2.08654061 -0.25212951
#> Br5889-H4a -1.4146639 -0.3514845 5.0184463 2.75141034 1.15700192
#> Br5889-H4b 3.4433652 2.1969559 3.3681149 3.88684088 -1.95214054
#> Br5889-H4c 15.9873176 3.7633527 4.0637448 4.31141121 -3.35253144
#> Br5889-H4d 19.5094658 7.4096739 5.9341236 1.80368304 -3.67381412
#> Br5941-H5a -22.0419158 1.5807285 8.1295078 -3.41247294 1.64470779
#> Br5941-H5b -8.8697237 5.6519260 5.8918015 -3.30879930 -0.38555744
#> Br5941-H5c -2.3678784 1.9300725 6.5161765 2.36053327 0.58450593
#> Br5941-H5d -3.0199792 3.4015244 7.5119565 -0.50574036 -0.41101206
#> Br2623-C1a -4.5199965 8.9249453 -2.7801294 -2.38976044 1.36556803
#> Br2623-C1b -9.3546218 9.5386242 -2.1276540 -3.95446968 0.46479482
#> Br2623-C1c -3.1657310 10.1323544 -2.7417267 -3.00703860 -0.03148605
#> Br2623-C1d 0.7736339 9.9680350 -3.2045912 -2.22683210 -0.24318779
#> Br5005-C2a -12.8475582 3.8741030 -5.3069843 0.14286265 5.26345205
#> Br5005-C2b -7.4429662 4.8847338 -6.1230187 0.12203656 3.48710335
#> Br5005-C2c -7.4277746 7.1227905 -6.4037019 -1.14615485 2.17730076
#> Br5005-C2d 2.2957480 7.5932940 -6.9834747 0.44091452 -0.41002468
#> Br5370-C3a 7.8626696 10.0100012 -2.4449842 -1.35874912 1.06817387
#> Br5370-C3b 11.3834946 10.2360201 -3.9916927 -0.32084631 -1.22874239
#> Br5370-C3c 16.9801608 11.3703756 -2.5986650 -0.53488319 -1.78817309
#> Br5370-C3d 19.3334321 10.1322825 -2.8902334 -0.36933264 -1.41092261
#> Br5889-C4a -3.9052788 2.8812354 -5.7253843 2.83609041 3.81624293
#> Br5889-C4b 2.2369303 3.6432344 -7.0027978 3.52195782 0.64948482
#> Br5889-C4c 9.2464010 6.9474427 -6.6720996 2.51806225 -1.26608458
#> Br5889-C4d 12.5556762 8.4500147 -5.4778069 3.32774688 -2.65883440
#> Br5941-C5a -1.7130276 6.6881252 -4.7813919 -0.70428838 1.84668374
#> Br5941-C5b -5.9645386 7.0068497 -4.1438332 -2.01879942 -0.15737483
#> Br5941-C5c -0.7358994 9.0086645 -4.9518412 -1.42215720 0.05585854
#> Br5941-C5d 4.1556194 8.2163381 -4.9923800 -0.66399321 -0.40064668
#> qSV6 qSV7 qSV8
#> DLPFC_Br1385_A1_ribo 1.06453573 -3.815556219 1.027593763
#> DLPFC_Br1385_A2_ribo -1.91660808 -0.373412600 1.557946934
#> DLPFC_Br1385_A3_ribo 0.82740993 -2.212276260 1.863476084
#> DLPFC_Br1385_A4_ribo 1.74505075 -1.115064084 2.834002112
#> DLPFC_Br1729_B1_ribo -0.27758192 -3.694350036 0.604497945
#> DLPFC_Br1729_B2_ribo 0.94333344 -2.300718429 0.833032270
#> DLPFC_Br1729_B3_ribo -2.81410074 0.164342146 0.410570144
#> DLPFC_Br1729_B4_ribo 0.76181246 0.899574264 -0.862819348
#> DLPFC_Br2015_F1_ribo -2.81227313 -0.543555516 2.975156750
#> DLPFC_Br2015_F2_ribo 0.60277590 -0.228855169 5.246330856
#> DLPFC_Br2015_F3_ribo 1.22030932 0.377111210 2.365659903
#> DLPFC_Br2015_F4_ribo -1.58251006 -0.195619129 2.428274741
#> DLPFC_Br2020_C1_ribo 1.59616912 -1.418234848 0.241582073
#> DLPFC_Br2020_C2_ribo 4.23857840 2.580718424 0.849556950
#> DLPFC_Br2020_C3_ribo -0.13360171 -0.056514286 0.156322719
#> DLPFC_Br2020_C4_ribo 3.72033921 3.082108375 0.744166153
#> DLPFC_Br2074_D1_ribo -2.17610415 -0.645713558 -3.357053282
#> DLPFC_Br2074_D2_ribo 1.94149150 -0.079358609 -4.692604532
#> DLPFC_Br2074_D3_ribo -1.74165236 2.971756749 -5.179630330
#> DLPFC_Br2074_D4_ribo 2.42652749 2.161298643 -5.173738926
#> Br2623-H1a 0.14637755 1.194930418 -0.672847932
#> Br2623-H1b 1.07979871 2.855834580 -0.695539948
#> Br2623-H1c 1.30163472 3.921330802 -1.267392877
#> Br2623-H1d 3.93193146 2.122686712 0.477239843
#> Br5005-H2a -1.65730262 -1.166873529 1.898825629
#> Br5005-H2b -1.59447123 1.378500228 1.368447893
#> Br5005-H2c -1.25019696 1.619695306 2.091350440
#> Br5005-H2d -0.61713110 0.336181957 2.790450433
#> Br5370-H3a -1.29379050 -1.989147917 -2.943435220
#> Br5370-H3b -0.82777172 0.270676633 -3.597173069
#> Br5370-H3c 0.12262276 -1.781037990 -1.454198677
#> Br5370-H3d 0.10683698 -3.182788886 -1.609341001
#> Br5889-H4a -3.75657200 -0.716657922 -2.659844471
#> Br5889-H4b -4.12240714 1.092508056 -1.645915017
#> Br5889-H4c -4.09234605 0.868814257 -1.101129325
#> Br5889-H4d -3.83254177 -0.687076820 0.371552020
#> Br5941-H5a 0.48467345 -1.650517932 1.662855093
#> Br5941-H5b 0.89532156 -0.004574709 1.280077530
#> Br5941-H5c 1.85917400 0.938641762 0.883438253
#> Br5941-H5d 1.58236376 0.438603339 2.639189967
#> Br2623-C1a 3.24585929 1.698399794 -1.420480730
#> Br2623-C1b 0.06200314 1.974004453 0.892435462
#> Br2623-C1c 3.06565524 2.293391255 -0.129613022
#> Br2623-C1d 3.04601058 2.985352440 -0.131862698
#> Br5005-C2a -0.99549421 -1.739838536 -0.192846850
#> Br5005-C2b -0.97955997 -0.228420366 0.821118120
#> Br5005-C2c -1.24089333 0.736576234 -0.182421919
#> Br5005-C2d -0.39937389 2.194399385 0.806529030
#> Br5370-C3a 2.24681796 -5.667046630 -2.196750720
#> Br5370-C3b 1.27472065 -4.087188119 -1.141386043
#> Br5370-C3c 2.13487792 -4.213819776 -1.267943503
#> Br5370-C3d 3.25956846 -5.574951123 -0.329608668
#> Br5889-C4a -3.26079690 -0.775653930 -1.637361337
#> Br5889-C4b -4.74726678 0.456974381 0.472426284
#> Br5889-C4c -4.48924614 1.891780432 0.376824968
#> Br5889-C4d -3.65896124 1.687838776 2.061090990
#> Br5941-C5a 1.52811658 0.653077397 -0.211566924
#> Br5941-C5b 0.53873097 1.041772240 0.864655602
#> Br5941-C5c 1.28614257 1.450106099 -0.139988199
#> Br5941-C5d 1.98298417 1.805836180 -0.002182388