A wrapper function used to perform qSVA in one step.
qSVA(
rse_tx,
type = c("cell_component", "standard", "top1500"),
sig_transcripts = select_transcripts(type),
mod,
assayname
)A RangedSummarizedExperiment-class object containing the transcript data desired to be studied.
a character string specifying which model you would like to use when selecting a degradation matrix.
A list of transcripts that are associated with
degradation signal. Use select_transcripts() to select sets of transcripts
identified by the qSVA expanded paper. Specifying a character() input of
ENSEMBL transcript IDs (or whatever values you have at rownames(rse_tx))
obtained outside of select_transcripts() overrides
the user friendly type argument. That is, this argument provides more fine
tuning options for advanced users.
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
## covComb_tx_deg 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(covComb_tx_deg)
)
## 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 = covComb_tx_deg, type = "cell_component", mod = mod, assayname = "tpm")
#> qSV1 qSV2 qSV3 qSV4
#> DLPFC_Br1385_A1_ribo -20.8283999 -18.9358162 11.8368597 -0.38990791
#> DLPFC_Br1385_A2_ribo 3.3372474 -17.1339387 2.2181715 1.73676021
#> DLPFC_Br1385_A3_ribo 35.3748653 -17.7544971 -5.5450016 -0.04749162
#> DLPFC_Br1385_A4_ribo 22.4269171 -20.3065083 4.2369380 1.48712394
#> DLPFC_Br1729_B1_ribo -25.0123011 -18.8415182 15.0132410 -0.70108704
#> DLPFC_Br1729_B2_ribo -15.1701602 -17.9420267 13.7012744 0.50581653
#> DLPFC_Br1729_B3_ribo 46.9207780 -22.2897020 0.4372831 -0.21605089
#> DLPFC_Br1729_B4_ribo 10.9413016 -22.0281930 12.7142861 0.08721363
#> DLPFC_Br2015_F1_ribo -29.3995258 -8.3544389 3.9805431 1.74773326
#> DLPFC_Br2015_F2_ribo -6.3204198 -10.4721078 6.4247990 2.18864116
#> DLPFC_Br2015_F3_ribo 15.7779525 -16.5898440 -4.4563884 0.50583992
#> DLPFC_Br2015_F4_ribo 11.2904985 -23.0349209 4.0765805 0.50995351
#> DLPFC_Br2020_C1_ribo -23.7013135 -16.3300484 9.4727160 2.79459708
#> DLPFC_Br2020_C2_ribo 7.1892335 -19.3861125 9.8201769 4.19523622
#> DLPFC_Br2020_C3_ribo 57.4179250 -24.7576640 -6.8127194 2.19078208
#> DLPFC_Br2020_C4_ribo 29.7637525 -21.1729343 5.4408057 4.11319713
#> DLPFC_Br2074_D1_ribo -43.8123596 -9.8948694 2.2809540 -1.54354325
#> DLPFC_Br2074_D2_ribo -19.3014354 -19.3799657 12.0356772 0.32831012
#> DLPFC_Br2074_D3_ribo 29.2666406 -31.4707974 3.8466814 -0.90302457
#> DLPFC_Br2074_D4_ribo -8.8774683 -19.9736883 9.5838997 -0.13659758
#> Br2623-H1a -29.5871404 -0.8983503 -11.0290341 -4.47414859
#> Br2623-H1b -15.4894971 0.1209622 -9.4141881 1.04938327
#> Br2623-H1c -15.9828262 -4.0485559 -10.6427513 -3.99206981
#> Br2623-H1d 3.6237689 -3.1175709 -16.2738209 -1.91615026
#> Br5005-H2a -38.3799917 2.8809254 4.9856222 -12.92133083
#> Br5005-H2b -9.3337908 8.7067971 10.2751425 -4.95540639
#> Br5005-H2c -18.4853856 3.5485338 1.8176085 -7.47678165
#> Br5005-H2d -6.5076058 6.0442811 -0.3228424 -9.91571964
#> Br5370-H3a -23.5888134 1.6245009 -8.2861373 -21.34840512
#> Br5370-H3b -1.4434709 4.1472788 -5.0481132 -16.94304366
#> Br5370-H3c 1.9617211 5.1906688 -6.7759051 -17.83768277
#> Br5370-H3d 17.8526682 2.7759192 -17.2175150 -21.15270193
#> Br5889-H4a -0.4701251 11.8751826 13.8751852 -11.41212989
#> Br5889-H4b 7.0633761 16.4422422 15.2495352 -7.23392242
#> Br5889-H4c 25.2251257 17.6023287 12.4713693 -6.87359313
#> Br5889-H4d 29.8482061 20.9653347 5.5102993 -6.43804434
#> Br5941-H5a -35.6253833 0.7134732 -10.5264167 -5.42196417
#> Br5941-H5b -17.6191395 2.5113135 -13.4322834 1.56757862
#> Br5941-H5c -6.6487252 -1.2955902 -9.5993058 0.78914386
#> Br5941-H5d -7.6194942 1.3309445 -13.6071695 -2.26065092
#> Br2623-C1a -10.1010034 3.4651972 -12.6639320 14.68966429
#> Br2623-C1b -12.7938639 13.1044541 -8.6413894 11.72388243
#> Br2623-C1c -6.8892598 5.5181045 -14.9853887 15.12509117
#> Br2623-C1d -0.6433381 5.7535892 -14.0623212 15.30292400
#> Br5005-C2a -18.5856349 10.7736928 7.0093586 3.88175527
#> Br5005-C2b -10.1477427 11.8512887 5.5053828 6.00909087
#> Br5005-C2c -11.2904273 12.5751571 3.0188303 7.33514500
#> Br5005-C2d 3.7343795 14.3375912 2.0946709 8.34727817
#> Br5370-C3a 11.1243523 14.9407954 -13.1933827 -7.11805206
#> Br5370-C3b 19.3258020 18.4608793 -11.4828406 -6.25664758
#> Br5370-C3c 25.8292091 15.8747211 -16.7403786 -6.34834583
#> Br5370-C3d 28.5445500 12.7132908 -19.2216966 -6.53677072
#> Br5889-C4a -0.9700789 21.7463078 22.4511925 3.15678553
#> Br5889-C4b 11.7991678 28.3404649 26.4469573 4.29122128
#> Br5889-C4c 21.2170851 31.2093559 22.3907290 5.21536455
#> Br5889-C4d 26.1076975 31.6279907 18.7055320 5.07813587
#> Br5941-C5a -4.6088301 4.6893368 -8.8994060 17.20439550
#> Br5941-C5b -8.3377268 10.1820536 -6.3878007 14.04295770
#> Br5941-C5c -3.2186105 6.8648876 -11.6051628 17.77800976
#> Br5941-C5d 3.8270681 4.8998134 -12.0550115 17.79225266
#> qSV5 qSV6 qSV7 qSV8
#> DLPFC_Br1385_A1_ribo 3.29894775 -1.8954415 4.83406406 -11.68699091
#> DLPFC_Br1385_A2_ribo 0.84142914 1.4315062 1.15898669 -16.89668243
#> DLPFC_Br1385_A3_ribo -1.23691206 9.2405143 1.60037940 -10.94782893
#> DLPFC_Br1385_A4_ribo -0.22938461 6.4807403 4.29630078 -12.12410484
#> DLPFC_Br1729_B1_ribo 4.75300439 -4.0030144 3.11435837 -4.92000092
#> DLPFC_Br1729_B2_ribo 4.51049214 -1.6362233 2.41412494 -5.16683186
#> DLPFC_Br1729_B3_ribo 0.56971055 5.7599980 -1.07249220 -5.43263053
#> DLPFC_Br1729_B4_ribo 3.16838318 -0.5522472 4.42032899 -0.20649712
#> DLPFC_Br2015_F1_ribo 3.41900549 -0.6198994 -0.73421338 -10.13414592
#> DLPFC_Br2015_F2_ribo 4.31215189 2.1610525 6.00198455 -1.42144827
#> DLPFC_Br2015_F3_ribo -0.40935541 8.6863557 -0.13533690 -2.25662222
#> DLPFC_Br2015_F4_ribo 4.94372727 3.4489181 -0.32213329 -4.96589724
#> DLPFC_Br2020_C1_ribo 1.46720062 -7.7961467 2.75399362 7.83051976
#> DLPFC_Br2020_C2_ribo 1.34470808 -6.3384212 5.19661754 12.62619357
#> DLPFC_Br2020_C3_ribo -3.81432346 4.5802790 -1.48774773 9.35572524
#> DLPFC_Br2020_C4_ribo -1.47191987 -3.2541064 2.09588336 13.76465289
#> DLPFC_Br2074_D1_ribo -1.75183563 -12.9689274 -10.11617641 -4.74763398
#> DLPFC_Br2074_D2_ribo 0.32398169 -13.1519853 -6.31620484 6.45949931
#> DLPFC_Br2074_D3_ribo -0.90696548 -5.2032692 -11.94930102 6.45550449
#> DLPFC_Br2074_D4_ribo -0.57767914 -11.4013011 -6.68290750 8.43098576
#> Br2623-H1a -12.69740447 1.9138557 -6.53451425 -1.75738761
#> Br2623-H1b -10.87797067 3.0498629 -7.11817127 0.93318134
#> Br2623-H1c -12.55090381 2.9803121 -6.44253868 1.52592184
#> Br2623-H1d -14.53239623 5.7884663 -8.67921032 1.79698709
#> Br5005-H2a 2.42068118 10.9512446 -0.12953474 2.41265702
#> Br5005-H2b 7.79465882 12.0175275 1.36284577 6.16517224
#> Br5005-H2c 6.76454127 14.1901712 -0.58747472 4.79404488
#> Br5005-H2d 3.38080691 14.3939315 2.02688893 6.22810083
#> Br5370-H3a 1.93037917 -5.7163601 0.71840260 -0.64194065
#> Br5370-H3b 5.25120934 -7.3121912 2.03259249 2.40058084
#> Br5370-H3c 3.55916337 -5.2554067 3.54218830 3.01837757
#> Br5370-H3d 2.96665210 -2.1553103 0.05010423 0.03320052
#> Br5889-H4a -12.72343611 1.6713121 -0.36124754 -0.05454226
#> Br5889-H4b -11.96667889 1.4334044 -0.59322297 0.32283968
#> Br5889-H4c -13.12566123 3.2421874 -1.88918750 0.55878449
#> Br5889-H4d -14.81789627 6.0559651 -2.18691163 -1.67350138
#> Br5941-H5a -9.28421469 1.3716811 8.20367336 -0.24067790
#> Br5941-H5b -10.17626423 0.8594806 9.46620221 -0.70811909
#> Br5941-H5c -10.71952941 1.1437176 12.15379216 4.57822866
#> Br5941-H5d -11.36542196 2.5073586 11.16092701 1.70449173
#> Br2623-C1a -1.90938499 -1.0596874 -10.57105777 -1.19942304
#> Br2623-C1b -3.48398945 -1.2994313 -6.77690867 -2.80423421
#> Br2623-C1c -2.03352754 -0.2720727 -10.96103824 -2.32973869
#> Br2623-C1d -2.57191628 -0.3600162 -10.48283360 -1.25557221
#> Br5005-C2a 15.07619837 8.8410781 -3.68414960 3.64808322
#> Br5005-C2b 16.94193248 11.3370314 -2.86233994 3.82357436
#> Br5005-C2c 15.77557559 11.3491061 -4.42787165 1.76588752
#> Br5005-C2d 15.90688141 11.2769542 -3.13208193 3.72499896
#> Br5370-C3a 12.76596963 -11.0755391 0.50262761 -2.74326702
#> Br5370-C3b 13.62213996 -11.0004558 1.01741797 -2.41919924
#> Br5370-C3c 12.98295147 -10.4774349 -0.88237918 -2.40960925
#> Br5370-C3d 14.87685298 -8.0954038 -1.53708193 -2.77389696
#> Br5889-C4a -2.19946861 -6.3500535 -1.17184592 -1.15574276
#> Br5889-C4b -3.81272604 -6.8604795 0.83932014 -1.91890775
#> Br5889-C4c -5.33064053 -5.3499233 -0.47747863 -3.04230493
#> Br5889-C4d -6.55865453 -4.0737780 0.22353501 -2.73816700
#> Br5941-C5a -0.06518356 -2.9455861 9.93025775 2.93378335
#> Br5941-C5b -1.40041323 -4.2474997 10.81490274 1.04866021
#> Br5941-C5c 0.22658203 -2.6394660 9.04720791 1.44201283
#> Br5941-C5d -0.59385989 -2.7969340 9.32568543 2.99089692
#> qSV9 qSV10
#> DLPFC_Br1385_A1_ribo 6.34511072 -4.1495011
#> DLPFC_Br1385_A2_ribo -1.92442917 -8.1839256
#> DLPFC_Br1385_A3_ribo 3.60630196 -6.2568901
#> DLPFC_Br1385_A4_ribo 7.54302269 -5.3148216
#> DLPFC_Br1729_B1_ribo 5.77893819 9.1803349
#> DLPFC_Br1729_B2_ribo 7.28928533 8.4832380
#> DLPFC_Br1729_B3_ribo -3.02450270 13.2738159
#> DLPFC_Br1729_B4_ribo 10.55883394 10.9141091
#> DLPFC_Br2015_F1_ribo -11.81402317 -6.5252192
#> DLPFC_Br2015_F2_ribo -4.91369086 -8.5616784
#> DLPFC_Br2015_F3_ribo -1.66189763 1.3488337
#> DLPFC_Br2015_F4_ribo -9.58395499 1.3503042
#> DLPFC_Br2020_C1_ribo 3.10327300 -7.9392924
#> DLPFC_Br2020_C2_ribo 7.02504464 -10.5244890
#> DLPFC_Br2020_C3_ribo -8.62780929 -4.9353544
#> DLPFC_Br2020_C4_ribo 7.29553174 -8.1189661
#> DLPFC_Br2074_D1_ribo -11.97889427 -2.7206437
#> DLPFC_Br2074_D2_ribo -1.96818749 0.1528716
#> DLPFC_Br2074_D3_ribo -13.77037563 9.1639410
#> DLPFC_Br2074_D4_ribo -0.86310922 0.7028271
#> Br2623-H1a 2.86676237 -0.2293483
#> Br2623-H1b 3.90817300 -1.6207157
#> Br2623-H1c 7.19468385 0.5193020
#> Br2623-H1d 3.64329853 -0.2277253
#> Br5005-H2a -3.15012947 0.2044681
#> Br5005-H2b 0.15519638 -1.4527198
#> Br5005-H2c 0.07232186 -3.7066066
#> Br5005-H2d -1.81868765 -1.8361417
#> Br5370-H3a 1.40711187 1.7683458
#> Br5370-H3b 3.56969060 0.9653862
#> Br5370-H3c 2.07156301 -2.4789929
#> Br5370-H3d 0.95105339 0.5577165
#> Br5889-H4a 1.65074195 4.8675765
#> Br5889-H4b 1.76308175 2.2874004
#> Br5889-H4c 1.27294612 1.6974219
#> Br5889-H4d -3.20788895 -0.8667641
#> Br5941-H5a -5.31164609 1.8319140
#> Br5941-H5b -4.06731484 2.7464987
#> Br5941-H5c -1.11500418 1.4189277
#> Br5941-H5d -4.74351709 0.3225908
#> Br2623-C1a 6.31286510 2.2224562
#> Br2623-C1b 0.76255820 -4.4206101
#> Br2623-C1c 4.95793090 -0.5068652
#> Br2623-C1d 5.05998073 -1.6079189
#> Br5005-C2a -0.84760437 3.0707237
#> Br5005-C2b -1.20533328 1.0742630
#> Br5005-C2c 0.09316461 2.6961947
#> Br5005-C2d -0.59410619 -0.5768293
#> Br5370-C3a 1.00753636 2.4760862
#> Br5370-C3b -0.34848194 -2.4107377
#> Br5370-C3c 0.82808073 -0.5304384
#> Br5370-C3d 1.12594882 -0.9059015
#> Br5889-C4a 0.79079185 4.5549161
#> Br5889-C4b -1.72577388 -2.3539147
#> Br5889-C4c -1.88028060 -1.6856983
#> Br5889-C4d -2.09381344 -4.2096251
#> Br5941-C5a -1.62961776 5.7478035
#> Br5941-C5b -3.73429788 0.4379703
#> Br5941-C5c -1.37779312 4.5531531
#> Br5941-C5d -1.02865899 4.2669448