An S4 class to store a SpaNorm model fit

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.

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>