getCellYield: Gets cell yield of each sample as a table

In KrishnaswamyLab/phemd: Phenotypic EMD for comparison of single-cell samples

Gets cell yield of each sample as a table

Description

Gets cell yield (number of viable cells) of each single-cell sample in decreasing order

Usage

getCellYield(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 cell yield of each 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)
getCellYield(my_phemdObj_final, cluster_assignments)

KrishnaswamyLab/phemd documentation built on Oct. 2, 2024, 5:10 a.m.