Screen for Interactions and Initialize Matchmaker Object

Source: R/matchmake.R

Screen for interactiins and initialize a Matchmaker object.

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

if (FALSE) {
object <- Screening(data = data.use, annotation = idents.use, interaction = interaction.data)
}