embedCells {phemd} | R Documentation |
Takes as input a Phemd object with aggregated data and returns updated object with Monocle2 object in @monocle_obj slot
embedCells(obj, data_model = "negbinomial_sz", ...)
obj |
'Phemd' object containing aggregated data |
data_model |
One of the following: 'negbinomial_sz', 'negbinomial', 'tobit', 'uninormal', 'gaussianff'. See "Family Function" table at the following link for more details on selecting the proper one. http://cole-trapnell-lab.github.io/monocle-release/docs/#getting-started-with-monocle |
... |
Additional parameters to be passed to |
Wrapper function for reduceDimension
in Monocle 2 package. aggregateSamples
needs to be called before running this function.
Same as input 'Phemd' object with additional Monocle2 object in @monocle_obj slot
my_phemdObj <- createDataObj(all_expn_data, all_genes, as.character(snames_data)) my_phemdObj_lg <- removeTinySamples(my_phemdObj, 10) my_phemdObj_lg <- aggregateSamples(my_phemdObj_lg, max_cells=1000) my_phemdObj_lg <- embedCells(my_phemdObj_lg, data_model = 'gaussianff', sigma=0.02, maxIter=2)