compareSamples {phemd} | R Documentation |
Takes as input a Phemd object with cell subtype relative frequencies for each sample in @data_cluster_weights slot and ground distance matrix (representing cell subtype pairwise dissimilarity) in @emd_dist_mat slot. Returns distance matrix representing pairwise dissimilarity between samples
compareSamples(obj)
obj |
'Phemd' object containing cell subtype relative frequencies for each sample in @data_cluster_weights slot and ground distance matrix (representing cell subtype dissimilarity) in @emd_dist_mat slot |
Requires 'transport' and 'pracma' packages
Distance matrix of dimension num_samples x num_samples representing pairwise dissimilarity between samples
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)