Estimate cell type compositions from a table of clone by cell type counts. Functions are provided for exploring the cell type compositions that are displayed by cell lineages. The workhorse is a function that performs blocked Gibbs sampling on the cell type frequencies in a parent population under a model that assumes a vague prior for the total number of cells and a uniform Dirichlet prior for the proportions fo different cell types.
You will need a fairly recent installation of R and the devtools
package and its dependencies.
library(devtools)
install_github( "BushmanLab/cellTypeCompositions",
ref="main",
build_vignettes=TRUE )The model implemented is described in the model vignette. After
installation of the package, enter the following lines at the R prompt:
library(cellTypeCompositions)
vignette( "model", "cellTypeCompositions")See the help page for the gibbsScan function. Run the example code for a start.