orderCellsMonocle: Compute Monocle2 cell state and pseudotime assignments
In phemd: Phenotypic EMD for comparison of single-cell samples

Description Usage Arguments Details Value Examples

Takes as input a Phemd object with Monocle2 object and returns updated object with Monocle2 object containing cell state and pseudotime assignments

1	orderCellsMonocle(obj, ...)

`obj`	'Phemd' object containing Monocle2 object initialized using embedCells
`...`	Additional parameters to be passed into `orderCells` function

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)