orderCellsMonocle {phemd}R Documentation

Compute Monocle2 cell state and pseudotime assignments

Description

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

Usage

orderCellsMonocle(obj, ...)

Arguments

obj

'Phemd' object containing initial Monocle 2 object

...

Additional parameters to be passed into orderCells function

Details

Wrapper function for orderCells in Monocle 2 package. embedCells needs to be called before calling this function.

Value

Same as input 'Phemd' object with updated Monocle2 object in @monocle_obj slot containing cell state and pseudotime assignments

Examples


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, data_model='gaussianff', sigma=0.02, maxIter=2)
my_phemdObj_monocle <- orderCellsMonocle(my_phemdObj_monocle)

[Package phemd version 1.0.0 Index]