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)A SingleCellAssay class object
A character specifying the factor for comparison
ignored
A character specifying the reference level of comparison.
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.
A logical specifying if additional rows should be returned with information about the different components of the test.
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
#> [ reached 'max' / getOption("max.print") -- omitted 59 rows ]