getSampleCelltypeFreqs {phemd} | R Documentation

## Returns cell subtype distribution for each sample as a table

### Description

Returns cell subtype distribution for each single-cell sample along with (optional) final inhibitor cluster assignment

### Usage

    getSampleCelltypeFreqs(myobj, cluster_assignments = NULL)

### Arguments

`myobj` | phemdObj object containing expression data for each sample in 'data' slot
`cluster_assignments` | Vector of cluster assignments to be included as additional column in output table (optional)

### Value

Data frame representing relative frequencies of each cell subtype along with (optional) final inhibitor cluster assignment for each single-cell sample

### 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)
    my_phemdObj_final <- clusterIndividualSamples(my_phemdObj_monocle)
    my_phemdObj_final <- generateGDM(my_phemdObj_final)
    my_EMD_mat <- compareSamples(my_phemdObj_final)
    cluster_assignments <- groupSamples(my_EMD_mat, distfun = 'hclust', ncluster=4)
    getSampleCelltypeFreqs(my_phemdObj_final, cluster_assignments)

[Package phemd version 1.0.1 Index]