createDataObj: Create 'Phemd' object
In phemd: Phenotypic EMD for comparison of single-cell samples

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

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

`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"

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

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

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

phemd documentation built on Nov. 8, 2020, 8:15 p.m.

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