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)

Arguments

sca

A SingleCellAssay class object

comparison

A character specifying the factor for comparison

...

ignored

referent

A character specifying the reference level of comparison.

groups

A optional character specifying a variable on which to stratify the test. For each level of groups, there will be a separate likelihood ratio test.

returnall

A logical specifying if additional rows should be returned with information about the different components of the test.

Value

data.frame

Details

Combined Likelihood ratio test (binomial and normal) for SingleCellAssay and derived objects. This function is deprecated, please use lrTest instead.

See also

zlm ZlmFit

Examples

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