@@ -3,6 +3,9 @@

 export(SpaNorm)

 export(fastSizeFactors)

 export(filterGenes)

+exportClasses(SpaNormFit)

+exportMethods("$")

+import(methods)

 importFrom(methods,is)

 importFrom(stats,dnbinom)

 importFrom(stats,mad)

@@ -1,3 +1,29 @@

+#' @name SpaNormFit

+#'

+#' @title An S4 class to store a SpaNorm model fit

+#' @slot ngenes a numeric, specifying the number of genes in the dataset.

+#' @slot ncells a numeric, specifying the number of cells/spots in the dataset.

+#' @slot gene.model a character, specifying the gene-specific model to used (see `getGeneModels()`).

+#' @slot df.tps an integer, specifying the degrees of freedom to used for the thin plate spline.

+#' @slot sample.p a numeric, specifying the proportion of samples used to approximated the model.

+#' @slot lambda.a a numeric, specifying the shinkage parameter used.

+#' @slot batch a vector or matrix, specifying the batch design used (if any). 

+#' @slot W a matrix, specifying the covariate matrix of the linear model.

+#' @slot alpha a matrix, specifying the coefficients of the linear model.

+#' @slot gmean a numeric, specifying the mean estimate for each gene in the linear model.

+#' @slot psi a numeric, specifying the over-dispersion parameter for each geneif a negative binomial model was used (or a vector of NAs if another gene model is used).

+#' @slot isbio a logical, specifying the columns of the covariate matrix that represent biology.

+#' @slot loglik a numeric, specifying the log-likelihood of the model at each external iteration.

+#' 

+#' @param x an object of class SpaNormFit.

+#' @param name a character, specifying the name of the slot to retrieve.

+#' @return Return value varies depending on method.

+#' @examples

+#' example(SpaNorm)

+NULL

+

+#' @export

+#' @import methods

 setClass(

   Class = "SpaNormFit",

   slots = c(

@@ -17,6 +43,8 @@ setClass(

   )

 )

+#' @rdname SpaNormFit

+#' @export

 setMethod(

   f = "$",

   signature = "SpaNormFit",

new file mode 100644

@@ -0,0 +1,53 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/AllClasses.R

+\name{SpaNormFit}

+\alias{SpaNormFit}

+\alias{$,SpaNormFit-method}

+\title{An S4 class to store a SpaNorm model fit}

+\usage{

+\S4method{$}{SpaNormFit}(x, name)

+}

+\arguments{

+\item{x}{an object of class SpaNormFit.}

+

+\item{name}{a character, specifying the name of the slot to retrieve.}

+}

+\value{

+Return value varies depending on method.

+}

+\description{

+An S4 class to store a SpaNorm model fit

+}

+\section{Slots}{

+

+\describe{

+\item{\code{ngenes}}{a numeric, specifying the number of genes in the dataset.}

+

+\item{\code{ncells}}{a numeric, specifying the number of cells/spots in the dataset.}

+

+\item{\code{gene.model}}{a character, specifying the gene-specific model to used (see \code{getGeneModels()}).}

+

+\item{\code{df.tps}}{an integer, specifying the degrees of freedom to used for the thin plate spline.}

+

+\item{\code{sample.p}}{a numeric, specifying the proportion of samples used to approximated the model.}

+

+\item{\code{lambda.a}}{a numeric, specifying the shinkage parameter used.}

+

+\item{\code{batch}}{a vector or matrix, specifying the batch design used (if any).}

+

+\item{\code{W}}{a matrix, specifying the covariate matrix of the linear model.}

+

+\item{\code{alpha}}{a matrix, specifying the coefficients of the linear model.}

+

+\item{\code{gmean}}{a numeric, specifying the mean estimate for each gene in the linear model.}

+

+\item{\code{psi}}{a numeric, specifying the over-dispersion parameter for each geneif a negative binomial model was used (or a vector of NAs if another gene model is used).}

+

+\item{\code{isbio}}{a logical, specifying the columns of the covariate matrix that represent biology.}

+

+\item{\code{loglik}}{a numeric, specifying the log-likelihood of the model at each external iteration.}

+}}

+

+\examples{

+example(SpaNorm)

+}