Tests for a change in ET binomial proportion or mean of positive ET Likelihood Ratio Test for SingleCellAssay objects
LRT(sca, comparison, ...) # S4 method for SingleCellAssay,character LRT(sca, comparison, referent = NULL, groups = NULL, returnall = FALSE)
sca | A |
---|---|
comparison | A |
... | ignored |
referent | A |
groups | A optional |
returnall | A |
data.frame
Combined Likelihood ratio test (binomial and normal) for SingleCellAssay and derived objects. This function is deprecated, please use lrTest instead.
zlm ZlmFit
data(vbetaFA) LRT(vbetaFA, 'Stim.Condition', 'Unstim')#> Stim.Condition test.type primerid lrstat direction p.value #> 1 Stim(SEB) comb B3GAT1 1.5622613 1 4.578880e-01 #> 2 Stim(SEB) comb BAX 8.0652869 1 1.772741e-02 #> 3 Stim(SEB) comb BCL2 4.7450627 1 9.324439e-02 #> 4 Stim(SEB) comb CCL2 0.7561235 1 6.851882e-01 #> 5 Stim(SEB) comb CCL3 9.2095911 1 1.000375e-02 #> 6 Stim(SEB) comb CCL4 13.8735075 1 9.714180e-04 #> 7 Stim(SEB) comb CCL5 1.7575976 1 4.152814e-01 #> 8 Stim(SEB) comb CCR2 2.8985299 1 2.347428e-01 #> 9 Stim(SEB) comb CCR4 3.3223886 1 1.899120e-01 #> 10 Stim(SEB) comb CCR5 4.6587323 1 9.735744e-02 #> 11 Stim(SEB) comb CCR7 39.1243255 -1 3.193454e-09 #> 12 Stim(SEB) comb CD109 11.1843027 1 3.727001e-03 #> 13 Stim(SEB) comb CD27 39.9679896 -1 2.094408e-09 #> 14 Stim(SEB) comb CD28 24.7306020 -1 4.264008e-06 #> 15 Stim(SEB) comb CD38 4.6791199 1 9.637004e-02 #> 16 Stim(SEB) comb CD3d 9.2052879 1 1.002529e-02 #> 17 Stim(SEB) comb CD3g 12.2316534 -1 2.207650e-03 #> 18 Stim(SEB) comb CD4 20.3969774 1 3.722654e-05 #> 19 Stim(SEB) comb CD40LG 47.1325025 1 5.825150e-11 #> 20 Stim(SEB) comb CD45 2.9793280 1 2.254484e-01 #> 21 Stim(SEB) comb CD48 22.0357926 -1 1.640546e-05 #> 22 Stim(SEB) comb CD5 35.8896419 -1 1.609397e-08 #> 23 Stim(SEB) comb CD69 59.6283282 1 1.126868e-13 #> 24 Stim(SEB) comb CD8a 1.9720800 1 3.730511e-01 #> 25 Stim(SEB) comb CSF1 14.1877582 1 8.301708e-04 #> 26 Stim(SEB) comb CSF2 12.4373631 1 1.991870e-03 #> 27 Stim(SEB) comb CTLA4 5.4613792 1 6.517433e-02 #> 28 Stim(SEB) comb CTSD 32.7168485 -1 7.863694e-08 #> 29 Stim(SEB) comb CXCL13 1.7895695 1 4.086956e-01 #> 30 Stim(SEB) comb CXCR4 24.7689912 -1 4.182942e-06 #> 31 Stim(SEB) comb DPP4 11.6187037 1 2.999373e-03 #> 32 Stim(SEB) comb ENTPD1 1.7560858 1 4.155955e-01 #> 33 Stim(SEB) comb EOMES 2.2173355 1 3.299983e-01 #> 34 Stim(SEB) comb FAS 6.2726399 1 4.344237e-02 #> 35 Stim(SEB) comb FASLG 12.6641628 1 1.778329e-03 #> 36 Stim(SEB) comb FOXP3 8.8656802 1 1.188070e-02 #> 37 Stim(SEB) comb GAPDH 41.8965729 1 7.984998e-10 #> 38 Stim(SEB) comb GATA3 7.2460169 1 2.670222e-02 #> 39 Stim(SEB) comb GZMA 0.4497203 -1 7.986279e-01 #> 40 Stim(SEB) comb HLADRA 4.5857404 1 1.009762e-01 #> 41 Stim(SEB) comb ICOS 1.6924939 1 4.290221e-01 #> 42 Stim(SEB) comb IFNg 19.0305726 1 7.371632e-05 #> 43 Stim(SEB) comb IL10 15.2728700 1 4.825457e-04 #> 44 Stim(SEB) comb IL12RbII 0.9040240 1 6.363465e-01 #> 45 Stim(SEB) comb IL13 6.8040022 1 3.330655e-02 #> 46 Stim(SEB) comb IL16 80.6806088 -1 3.022932e-18 #> 47 Stim(SEB) comb IL2 21.4202359 1 2.231798e-05 #> 48 Stim(SEB) comb IL22 10.0688053 1 6.510086e-03 #> 49 Stim(SEB) comb IL2Ra 16.5345877 1 2.567792e-04 #> 50 Stim(SEB) comb IL2Rg 27.3758616 -1 1.136075e-06 #> 51 Stim(SEB) comb IL3 4.0516709 1 1.318836e-01 #> 52 Stim(SEB) comb IL4 4.9644775 1 8.355595e-02 #> 53 Stim(SEB) comb IL6R 45.7493495 -1 1.163202e-10 #> 54 Stim(SEB) comb IL6ST 13.8079441 -1 1.003790e-03 #> 55 Stim(SEB) comb IL7R 12.6296402 -1 1.809291e-03 #> 56 Stim(SEB) comb IL8 9.7769904 1 7.532749e-03 #> 57 Stim(SEB) comb LIF 16.0247377 1 3.313389e-04 #> 58 Stim(SEB) comb MKI67 1.3405178 1 5.115761e-01 #> 59 Stim(SEB) comb MMP9 11.2754562 -1 3.560949e-03 #> 60 Stim(SEB) comb NT5E 2.6568509 1 2.648940e-01 #> 61 Stim(SEB) comb PCNA 3.2187139 1 2.000162e-01 #> 62 Stim(SEB) comb PECAM1 1.7650930 1 4.137280e-01 #> 63 Stim(SEB) comb PRDM1 10.3503530 1 5.655219e-03 #> 64 Stim(SEB) comb PRF1 2.5049682 1 2.857940e-01 #> 65 Stim(SEB) comb RORC 4.0621171 1 1.311966e-01 #> 66 Stim(SEB) comb SLAMF1 9.8238721 1 7.358229e-03 #> 67 Stim(SEB) comb SLAMF5 2.4285892 1 2.969194e-01 #> 68 Stim(SEB) comb SLAMF7 4.9270545 1 8.513413e-02 #> 69 Stim(SEB) comb TBX21 3.5895831 1 1.661621e-01 #> 70 Stim(SEB) comb TGFB1 17.1380553 1 1.898972e-04 #> 71 Stim(SEB) comb TIA1 5.2156846 1 7.369338e-02 #> 72 Stim(SEB) comb TIMP1 4.6041022 1 1.000534e-01 #> 73 Stim(SEB) comb TNF 32.3906762 1 9.256654e-08 #> 74 Stim(SEB) comb TNFRSF9 23.7068304 1 7.114218e-06 #> 75 Stim(SEB) comb TNFSF10 5.7445662 -1 5.656962e-02