subsetCellChat: Subset CellChat object using a portion of cells

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

Subset CellChat object using a portion of cells

Description

Subset CellChat object using a portion of cells

Usage

subsetCellChat(
  object,
  cells.use = NULL,
  idents.use = NULL,
  group.by = NULL,
  invert = FALSE,
  thresh = 0.05
)

Arguments

object	A CellChat object (either an object from a single dataset or a merged objects from multiple datasets)
cells.use	a char vector giving the cell barcodes to subset. If cells.use = NULL, USER must define 'idents.use'
idents.use	a subset of cell groups used for analysis
group.by	cell group information; default is 'object@idents'; otherwise it should be one of the column names of the meta slot
invert	whether invert the idents.use
thresh	threshold of the p-value for determining significant interaction. A parameter as an input of the function 'computeCommunProbPathway'

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.