orderCellsMonocle {phemd} | R Documentation |
Takes as input a Phemd object with Monocle2 object and returns updated object with Monocle2 object containing cell state and pseudotime assignments
orderCellsMonocle(obj, ...)
obj |
'Phemd' object containing Monocle2 object initialized using embedCells |
... |
Additional parameters to be passed into |
Wrapper function for orderCells
in Monocle 2 package. embedCells
needs to be called before calling this function.
Same as input 'Phemd' object with updated cell-state embedding object containing cell state assignments
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_monocle <- embedCells(my_phemdObj_lg, cell_model='monocle2', data_model='gaussianff', sigma=0.02, maxIter=2) my_phemdObj_monocle <- orderCellsMonocle(my_phemdObj_monocle)