getSampleCelltypeFreqs {phemd} | R Documentation |
Returns cell subtype distribution for each single-cell sample along with (optional) final inhibitor cluster assignment
getSampleCelltypeFreqs(myobj, cluster_assignments = NULL)
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) |
Data frame representing relative frequencies of each cell subtype along with (optional) final inhibitor cluster assignment for each single-cell sample
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)