Using the pcs and the k number of components be included, we generate the qsva matrix.
get_qsvs(qsvPCs, k)prcomp object generated by taking the pcs of degraded transcripts
number of qsvs to be included.
matrix with k principal components for each sample.
qsv <- getPCs(rse_tx, "tpm")
get_qsvs(qsv, 2)
#> qSV1 qSV2
#> DLPFC_Br1385_A1_ribo -20.8283999 -18.9358162
#> DLPFC_Br1385_A2_ribo 3.3372474 -17.1339387
#> DLPFC_Br1385_A3_ribo 35.3748653 -17.7544971
#> DLPFC_Br1385_A4_ribo 22.4269171 -20.3065083
#> DLPFC_Br1729_B1_ribo -25.0123011 -18.8415182
#> DLPFC_Br1729_B2_ribo -15.1701602 -17.9420267
#> DLPFC_Br1729_B3_ribo 46.9207780 -22.2897020
#> DLPFC_Br1729_B4_ribo 10.9413016 -22.0281930
#> DLPFC_Br2015_F1_ribo -29.3995258 -8.3544389
#> DLPFC_Br2015_F2_ribo -6.3204198 -10.4721078
#> DLPFC_Br2015_F3_ribo 15.7779525 -16.5898440
#> DLPFC_Br2015_F4_ribo 11.2904985 -23.0349209
#> DLPFC_Br2020_C1_ribo -23.7013135 -16.3300484
#> DLPFC_Br2020_C2_ribo 7.1892335 -19.3861125
#> DLPFC_Br2020_C3_ribo 57.4179250 -24.7576640
#> DLPFC_Br2020_C4_ribo 29.7637525 -21.1729343
#> DLPFC_Br2074_D1_ribo -43.8123596 -9.8948694
#> DLPFC_Br2074_D2_ribo -19.3014354 -19.3799657
#> DLPFC_Br2074_D3_ribo 29.2666406 -31.4707974
#> DLPFC_Br2074_D4_ribo -8.8774683 -19.9736883
#> Br2623-H1a -29.5871404 -0.8983503
#> Br2623-H1b -15.4894971 0.1209622
#> Br2623-H1c -15.9828262 -4.0485559
#> Br2623-H1d 3.6237689 -3.1175709
#> Br5005-H2a -38.3799917 2.8809254
#> Br5005-H2b -9.3337908 8.7067971
#> Br5005-H2c -18.4853856 3.5485338
#> Br5005-H2d -6.5076058 6.0442811
#> Br5370-H3a -23.5888134 1.6245009
#> Br5370-H3b -1.4434709 4.1472788
#> Br5370-H3c 1.9617211 5.1906688
#> Br5370-H3d 17.8526682 2.7759192
#> Br5889-H4a -0.4701251 11.8751826
#> Br5889-H4b 7.0633761 16.4422422
#> Br5889-H4c 25.2251257 17.6023287
#> Br5889-H4d 29.8482061 20.9653347
#> Br5941-H5a -35.6253833 0.7134732
#> Br5941-H5b -17.6191395 2.5113135
#> Br5941-H5c -6.6487252 -1.2955902
#> Br5941-H5d -7.6194942 1.3309445
#> Br2623-C1a -10.1010034 3.4651972
#> Br2623-C1b -12.7938639 13.1044541
#> Br2623-C1c -6.8892598 5.5181045
#> Br2623-C1d -0.6433381 5.7535892
#> Br5005-C2a -18.5856349 10.7736928
#> Br5005-C2b -10.1477427 11.8512887
#> Br5005-C2c -11.2904273 12.5751571
#> Br5005-C2d 3.7343795 14.3375912
#> Br5370-C3a 11.1243523 14.9407954
#> Br5370-C3b 19.3258020 18.4608793
#> Br5370-C3c 25.8292091 15.8747211
#> Br5370-C3d 28.5445500 12.7132908
#> Br5889-C4a -0.9700789 21.7463078
#> Br5889-C4b 11.7991678 28.3404649
#> Br5889-C4c 21.2170851 31.2093559
#> Br5889-C4d 26.1076975 31.6279907
#> Br5941-C5a -4.6088301 4.6893368
#> Br5941-C5b -8.3377268 10.1820536
#> Br5941-C5c -3.2186105 6.8648876
#> Br5941-C5d 3.8270681 4.8998134