Description Usage Arguments Value
Perform a regression with reg_vgam
or reg_loess
function and compute p-values based on a likelihood ratio test as well as a AIC based criteria (computation of the difference of AIC between the null model and the alternative model).
1 2 | likelihood_criteria(data, gene, reg.f = "loess", pval = F, span = 0.75,
s.df = 4, fam = "gaussian", dtw = F)
|
data |
a |
gene |
character, a gene of interest. |
reg.f |
the regression method to use, either "loess" with the gam package, "ns" which fits a natural cubic spline with gam package or "splines" which fits a smoothing spline (default is "loess"). |
pval |
logical, if the likelihood criteria is to be computed or not (default is FALSE). |
span |
numeric, a smoothing parameter for the regression function (default is 0.75, see |
s.df |
numeric, a smoothing parameter for the nsplines regregression (default is 4, see |
fam |
character, for the vgam regression, the distribution assumption of the residuals; etiher "binomial" or "gaussian" (default is "gaussian"). |
dtw |
logical, if the alignment should be made with dtw before acomputing the likelihood, (default is FALSE) . |
returns the pvalue and if asked the aic difference for the gene of intereset.
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