getSampleCelltypeFreqs: Returns cell subtype distribution for each sample as a table

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

Returns cell subtype distribution for each sample as a table

Description

Returns cell subtype distribution for each single-cell sample along with (optional) final inhibitor cluster assignment

Usage

getSampleCelltypeFreqs(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 relative frequencies of each cell subtype along with (optional) final inhibitor cluster assignment for each single-cell 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)
getSampleCelltypeFreqs(my_phemdObj_final, cluster_assignments)

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