gating_model: Model creation and editing

In scGate: Marker-Based Cell Type Purification for Single-Cell Sequencing Data

Model creation and editing

Description

Generate an scGate model from scratch or edit an existing one

Usage

gating_model(
  model = NULL,
  level = 1,
  name,
  signature,
  positive = TRUE,
  negative = FALSE,
  remove = FALSE
)

Arguments

model	scGate model to be modified. When is NULL (default) a new model will be initialized.
level	integer. It refers to the hierarchical level of the model tree in which the signature will be added (level=1 by default)
name	Arbitrary signature name (i.e. Immune, Tcell, NK etc).
signature	character vector indicating gene symbols to be included in the signature (e.g. CD3D). If a minus sign is placed to the end of a gene name (e.g. "CD3D-"), this gene will be used as negative in UCell computing. See UCell documentation for details
positive	Logical indicating if the signature must be used as a positive signature in those model level. Default is TRUE.
negative	Same as 'positive' but negated (negative=TRUE equals to positive=FALSE)
remove	Whether to remove the given signature from the model

Value

A scGate model that can be used by scGate to filter target cell types.

Examples

# create a simple gating model
my_model <- gating_model(level = 1, name = "immune", signature = c("PTPRC"))
my_model <- gating_model(model = my_model, level = 1, positive = FALSE,
    name = "Epithelial", signature = c("CDH1","FLT1") )
# Remove an existing signature
dropped_model <- gating_model(model = my_model, remove =TRUE, level = 1, name = "Epithelial")

scGate documentation built on May 29, 2024, 2:56 a.m.