Description Usage Arguments Details Value References See Also Examples
Function to fit a linear mixed effect model splines to perform differential expression analysis. The lmmsDE
function fits LMM models with either a cubic
, p-spline
or cubic p-spline
basis and compares the models to the null models. The type of basis to use is specified with the basis
argument.
1 2 |
data |
|
time |
|
sampleID |
|
group |
|
type |
|
experiment |
|
basis |
|
knots |
can take an integer value corresponding to the number of knots for the chosen basis or by default calculated as in Ruppert 2002. Not in use for the 'cubic' smoothing spline basis. |
keepModels |
alternative |
numCores |
alternative |
lmmsDE extends the LMMS modelling framework to permit tests between groups, across time, and for interactions between the two implemented as described in Straube et al. 2015.
lmmsDE returns an object of class lmmsde
containing the following components:
DE |
|
modelsUsed |
|
predTime |
|
predGroup |
|
predTime |
|
predTimeGroup |
|
modelTime |
a |
modelGroup |
a |
modelTimeGroup |
a |
type |
an object of class |
experiment |
an object of class |
Durban, M., Harezlak, J., Wand, M. P., & Carroll, R. J. (2005). Simple fitting of subject-specific curves for longitudinal data. Stat. Med., 24(8), 1153-67.
Ruppert, D. (2002). Selecting the number of knots for penalized splines. J. Comp. Graph. Stat. 11, 735-757
Verbyla, A. P., Cullis, B. R., & Kenward, M. G. (1999). The analysis of designed experiments and longitudinal data by using smoothing splines. Appl.Statist, 18(3), 269-311.
Straube J., Gorse A.-D., Huang B.E., & Le Cao K.-A. (2015). A linear mixed model spline framework for analyzing time course 'omics' data PLOSONE, 10(8), e0134540.
1 2 3 4 5 6 | ## Not run:
data(kidneySimTimeGroup)
lmmsDEtest <-lmmsDE(data=kidneySimTimeGroup$data,time=kidneySimTimeGroup$time,
sampleID=kidneySimTimeGroup$sampleID,group=kidneySimTimeGroup$group)
summary(lmmsDEtest)
## End(Not run)
|
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