Phemd: Phemd class

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

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

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