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 1.1.1 Index]