Description Usage Arguments Details Value Examples
View source: R/functions-getResults.R
Takes vector of cluster assignments and phemdObj containing sample names and writes sample groups to file
1 | printClusterAssignments(cluster_assignments, obj, dest, overwrite = FALSE)
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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 |
Order of samples in obj@snames is assumed to be the same as the order of group assignments in cluster_assignments
None
1 2 3 4 5 6 7 8 9 10 | 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)
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