orderCellsMonocle: Compute Monocle2 cell state and pseudotime assignments

In wschen/phemd: Phenotypic EMD for comparison of single-cell samples

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 Monocle2 object initialized using embedCells
...	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 cell-state embedding object containing cell state 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, cell_model='monocle2', data_model='gaussianff', sigma=0.02, maxIter=2)
my_phemdObj_monocle <- orderCellsMonocle(my_phemdObj_monocle)

wschen/phemd documentation built on April 8, 2023, 6:27 a.m.