R/data.R

In compbiomed/celda: CEllular Latent Dirichlet Allocation

#' A toy count matrix for use with celda. 
#'
#' @title sample.cells
#' @description A matrix of simulated gene counts
#' @format A matrix of simulated gene counts with 10 rows (genes) and 10 columns
#' (cells)
#' @details Generated by Josh Campbell
#' @source \url{http://github.com/definitelysean/celda}
"sample.cells"

#' An example simulated count matrix from the celda_CG model.
#' 
#' @title celda.CG.sim
#' @format A list of counts and properties as returned from simulateCells()
#' @examples 
#' celda.CG.sim = simulateCells("celda_CG")
"celda.CG.sim"

#' A toy contamination data generated by simulateObservedMatrix
#'
#' @title contamination.sim
#' @description Generated by simulateObservedMatrix
#' @format A list
"contamination.sim"

#' celda_CG results generated from celda.CG.sim
#' 
#' @title celda.CG.mod
#' @format A celda_CG object
#' @examples 
#' celda.CG.mod = celda_CG(celda.CG.sim$counts, K=celda.CG.sim$K,
#'                         L=celda.CG.sim$L, nchains=1)
"celda.CG.mod"

#' Example results of celdaGridSearch on celda.CG.sim
#' @title celda.CG.grid.search.res
#' @format An object as returned from celdaGridSearch()
#' @examples
#' cgs = celdaGridSearch(celda.CG.sim$counts, model="celda_CG", 
#'                       params.test=list(K=4:6, L=9:11), 
#'                       params.fixed=list(sample.label=celda.CG.sim$sample.label),
#'                       best.only=TRUE, nchains=1)
"celda.CG.grid.search.res"


#' An example simulated count matrix from the celda_C model.
#' 
#' @title celda.C.sim
#' @format A list of counts and properties as returned from simulateCells()
#' @examples 
#' celda.C.sim = simulateCells("celda_C")
"celda.C.sim"

#' celda_C results generated from celda.C.sim
#' 
#' @title celda.C.mod
#' @format A celda_C object
#' @examples 
#' celda.C.mod = celda_C(celda.C.sim$counts, K=celda.C.sim$K, nchains=1)
"celda.C.mod"

#' An example simulated count matrix from the celda_G model.
#' 
#' @title celda.G.sim
#' @format A list of counts and properties as returned from simulateCells()
#' @examples 
#' celda.G.sim = simulateCells("celda_G")
"celda.G.sim"

#' celda_G results generated from celda.G.sim
#' 
#' @title celda.G.mod
#' @format A celda_G object
#' @examples 
#' celda.G.mod = celda_G(celda.G.sim$counts, L=celda.G.sim$L, nchains=1)
"celda.G.mod"