countland-class: An S4 class to represent a countland object

In countland: Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq

An S4 class to represent a countland object

Description

An S4 class to represent a countland object

Slots

counts

A dgCMatrix with rows as cells, columns as genes.

names_genes

A character vector of column names.

names_cells

A character vector of row names.

raw_counts

The count dgCMatrix as originally loaded.

raw_names_genes

The gene name character vector as originally loaded.

raw_names_cells

The cell name character vector as originally loaded.

subsample

A dgCMatrix with row sums equal.

cell_scores

A data.frame of cell count measures.

gene_scores

A data.frame of gene expression measures.

dots

A similarity dgCMatrix of dot products.

eigenvals

An vector of eigenvalues from spectral embedding

embedding

An array of two columns (spectral embeddings).

cluster_labels

A numeric vector of cluster assignments of length n cells.

marker_full

A list of data.frames with genes ranked for each cluster.

marker_genes

A data.frame of top ten marker genes per cluster.

matrixU

A dgCMatrix of dimensions cells x features.

matrixV

A dgCMatrix of dimensions genes x features.

matrixLambda

A diagonal dgCMatrix of scaling factors.

sharedcounts

A similarity dgCMatrix of shared counts between genes.

sum_sharedcounts

A dgCMatrix with counts summed within gene clusters.

sum_sharedcounts_all

A dgCMatrix with counts summed and including all genes not present in any cluster.

norm_factor

A numeric vector of cell normalization factors.

norm_counts

A dgCMatrix of normalized counts.

log_counts

A dgCMatrix of log transformed counts.

scaled_counts

A dgCMatrix of counts scaled by gene unit variance.

centered_counts

A dgCMatrix of counts centered at zero.

verbose

A T/F object for suppressing messages

countland documentation built on May 29, 2024, 7:13 a.m.