Screening: Screen for Interactions and Initialize Matchmaker Object

In stevexniu/scMatchmaker: Single Cell Matchmaker

Screen for Interactions and Initialize Matchmaker Object

Description

Screen for interactiins and initialize a Matchmaker object.

Usage

Screening(
  data,
  annotation,
  interaction,
  partner_a = 1,
  partner_b = 2,
  path = FALSE,
  project_name = "",
  zero_percent = 0.7
)

Arguments

data	Expression data. A d x M matrix with d rows of features and M columns of data points (cells).
annotation	Cell type identity in following formats: character, cell type identity with either names as cell ids (barcodes) or in the same order matching the column names in data. data.frame, cell ids (barcodes) in row names and cell type identity in first column.
interaction	Interaction partner pair data with at least two columns indicating gene-gene interaction partners.
partner_a	Column name or index for interaction partner a. Defaulte is 1, the first column in interaction pair data.
partner_b	Column name or index for interaction partner b. Defaulte is 2, the second column in interaction pairs data.
path	Whether inputs are in directory path format.
project_name	Name of the project.
zero_percent	Zero-entry percentage threshold. If the number of zero entries in the returned matrices is above this number, a sparse matrix will be returned. Default is 0.7 aka 70%.

Value

Returns a Matchmaker object.

Examples

## Not run: 
object <- Screening(data = data.use, annotation = idents.use, interaction = interaction.data)

## End(Not run)

stevexniu/scMatchmaker documentation built on June 2, 2022, 12:35 p.m.