printClusterAssignments {phemd} | R Documentation

## Writes samples to file based on community detection group assignments

### Description

Takes vector of cluster assignments and phemdObj containing sample names and writes sample groups to file

### Usage

    printClusterAssignments(cluster_assignments, obj, dest,
      overwrite = FALSE)

### Arguments

`cluster_assignments` | Vector containing group assignments for each sample
`obj` | phemdObj object containing sample names in @snames slot
`dest` | Path to existing directory where output should be saved
`overwrite` | Boolean representing whether or not to overwrite contents of "dest" with output of printClusterAssignments

### Details

Order of samples in obj@snames is assumed to be the same as the order of group assignments in cluster_assignments

### Value

None

### 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)
    printClusterAssignments(cluster_assignments, my_phemdObj_final, '.', overwrite=TRUE)

[Package phemd version 1.1.1 Index]