embedCells {phemd} | R Documentation

## Generate Monocle2 embedding

### Description

Takes as input a Phemd object with aggregated data and returns updated object with Monocle2 object in @monocle_obj slot

### Usage

    embedCells(obj, data_model = "negbinomial_sz", ...)

### Arguments

`obj` | 'Phemd' object containing aggregated data
`data_model` | One of the following: 'negbinomial_sz', 'negbinomial', 'tobit', 'uninormal', 'gaussianff'. See "Family Function" table at the following link for more details on selecting the proper one. http://cole-trapnell-lab.github.io/monocle-release/docs/#getting-started-with-monocle
`...` | Additional parameters to be passed to `reduceDimension` function

### Details

Wrapper function for `reduceDimension` in Monocle 2 package. `aggregateSamples` needs to be called before running this function.

### Value

Same as input 'Phemd' object with additional Monocle2 object in @monocle_obj slot

### 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_lg <- embedCells(my_phemdObj_lg, data_model = 'gaussianff', sigma=0.02, maxIter=2)

[Package phemd version 1.0.1 Index]