Phemd {phemd} | R Documentation

## Phemd class

### Description

The main PhEMD class to store single-cell expression data.

### Fields

`data`

  List of matrices, each of which represents a single-cell sample (num_cells x num_genes)

`markers`

  Column names (e.g. genes) for each element (i.e. data matrix) in "data"

`snames`

  Sample ID for each element in "data"

`data_aggregate`

  Numeric matrix representing expression data for cells from all experimental conditions (rows = markers, cols = cells)

`data_subsample_idx`

  List of vectors each representing the indices of elements in "data" that were subsampled and combined to form "data_aggregate"

`subsampled_bool`

  Boolean represent whether or not subsampling was performed in the data aggregation process

`monocle_obj`

  Data object of type "CellDataSet" that is the core Monocle data structure

`data_cluster_weights`

  Matrix representing cell subtype relative frequencies for each sample (num_samples x num_genes)

`emd_dist_mat`

  Matrix representing pairwise distances between each pair of cell subtypes

`seurat_obj`

  Object of class "Seurat" that is the core Seurat data structure

`phate_obj`

  Object of class "phate" that is the core PHATE data structure

`experiment_ids`

  Vector of length num_samples representing the experiment (batch) in which the sample was profiled

[Package phemd version 1.3.0 Index]