make.cell.type: make.cell.type

In livnatje/DIALOGUE: DIALOGUE is a dimensionality reduction algorithm that uses cross-cell-type associations to identify multicellular programs and map the cell transcriptome as a function of its environment.

make.cell.type

Description

This function generates a cell.type object for DIALOGUE.

Usage

make.cell.type(
  name,
  tpm,
  samples,
  X = NULL,
  metadata = NULL,
  tpmAv = t(average.mat.rows(t(tpm), samples)),
  cellQ
)

Arguments

name	cell type name
tpm	gene expression or any type of single-cell profiling (m x n)
samples	the sample of each cell (n x 1)
X	features matrix (n x k), e.g., PCs, NMF components, tpm etc.; these features will be used to identify the multicellular programs.
metadata	cell features (n x r)
cellQ	cell quality measures, e.g., number of reads/genes detected (n x 1)

Fields

cell.type

a representation of a specific type of cells

livnatje/DIALOGUE documentation built on Jan. 30, 2024, 1:31 a.m.