createIngresObject: Create a new 'ingres' object.

In ingres: Infer Gene Probabilistic Boolean Networks from Single-Cell Data

Create a new ingres object.

Description

Create a new ingres object.

Usage

createIngresObject(expression.matrix, idents, network.genes, network)

Arguments

expression.matrix	A single-cell expression matrix, with cells in rows and genes in columns.
idents	A data frame with a column for cell barcode and another column for the corresponding cluster or subpopulation.
network.genes	A data frame with a column for node names and another column for the corresponding entrez IDs.
network	A object of class tbl_graph representing our network of interest.

Value

An ingres object.

Examples

# Get expression matrix from small_blca_wang for convenience, but it can be
# any single-cell expression matrix, from any source. Same for idents.
expression.matrix =
  as.matrix(Seurat::GetAssayData(
    small_blca_wang,
    assay = "RNA", slot = "data"
  ))

idents = data.frame(
  cell = names(Seurat::Idents(small_blca_wang)),
  cluster = as.character(Seurat::Idents(small_blca_wang)),
  check.names = FALSE
)

ing = createIngresObject(expression.matrix, idents, network_genes, network)
ing

ingres documentation built on Sept. 14, 2022, 9:05 a.m.