An S4 class to store a SpaNorm model fit

Usage

# S4 method for class 'SpaNormFit'
x$name

Arguments

x: an object of class SpaNormFit.
name: a character, specifying the name of the slot to retrieve.

Value

Return value varies depending on method.

Slots

ngenes: a numeric, specifying the number of genes in the dataset.
ncells: a numeric, specifying the number of cells/spots in the dataset.
gene.model: a character, specifying the gene-specific model to used (see getGeneModels()).
df.tps: an integer, specifying the degrees of freedom to used for the thin plate spline.
sample.p: a numeric, specifying the proportion of samples used to approximated the model.
lambda.a: a numeric, specifying the shinkage parameter used.
batch: a vector or matrix, specifying the batch design used (if any).
W: a matrix, specifying the covariate matrix of the linear model.
alpha: a matrix, specifying the coefficients of the linear model.
gmean: a numeric, specifying the mean estimate for each gene in the linear model.
psi: a numeric, specifying the over-dispersion parameter for each gene if a negative binomial model was used (or a vector of NAs if another gene model is used).
wtype: a factor, specifying the covariate types of columns in the covariate matrix, W. These could be "biology", "ls", or "batch".
loglik: a numeric, specifying the log-likelihood of the model at each external iteration.
sampling: a factor, specifying the cells/spots used for dispersion estimation ('dispersion'), GLM fitting ('glm' and 'dispersion'), all other cells/spots ('all').

Examples

example(SpaNorm)
#> 
#> SpaNrm> data(HumanDLPFC)
#> 
#> SpaNrm> ## No test: 
#> SpaNrm> ##D SpaNorm(HumanDLPFC, sample.p = 0.05, df.tps = 2, tol = 1e-2)
#> SpaNrm> ## End(No test)
#> SpaNrm> 
#> SpaNrm> 
#> SpaNrm>