createDataObj: Create 'Phemd' object

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

Create 'Phemd' object

Description

Wrapper function to create 'Phemd' object containing raw expression data and metadata

Usage

createDataObj(data, markers, snames, datatype = "list", valtype = "counts")

Arguments

data	List of length num_samples containing expression data; each element is of size num_cells x num_markers. Alternately a SingleCellExperiment object.
markers	Vector containing marker names (i.e. column names of all_data)
snames	Vector containing sample names (i.e. names of samples contained in all_data)
datatype	Either "list" or "sce" (SingleCellExperiment with genes x cells)
valtype	Type of assay data (i.e. "counts", "normcounts", "logcounts", "tpm", "cpm") if datatype is "sce"

Details

Note that each element in list can have different number of rows (i.e. number of cells in each sample can vary).

Value

'Phemd' object containing raw multi-sample expression data and associated metadata

Examples

my_phemdObj <- createDataObj(all_expn_data, all_genes, as.character(snames_data))

KrishnaswamyLab/phemd documentation built on April 24, 2023, 3:50 p.m.