computeAveExpr: Compute averaged expression values for each cell group

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

Compute averaged expression values for each cell group

Description

Compute averaged expression values for each cell group

Usage

computeAveExpr(
  object,
  features = NULL,
  group.by = NULL,
  type = c("triMean", "truncatedMean", "median"),
  trim = NULL,
  slot.name = c("data.signaling", "data"),
  data.use = NULL
)

Arguments

object	CellChat object
features	a char vector giving the used features. default use all features
group.by	cell group information; default is 'object@idents' when input is a single object and 'object@idents$joint' when input is a merged object; otherwise it should be one of the column names of the meta slot
type	methods for computing the average gene expression per cell group. By default = "triMean", defined as a weighted average of the distribution's median and its two quartiles (https://en.wikipedia.org/wiki/Trimean); When setting ‘type = "truncatedMean"', a value should be assigned to ’trim'. See the function 'base::mean'.
trim	the fraction (0 to 0.25) of observations to be trimmed from each end of x before the mean is computed.
slot.name	the data in the slot.name to use
data.use	a customed data matrix. Default: data.use = NULL and the expression matrix in the 'slot.name' is used

Value

Returns a matrix with genes as rows, cell groups as columns.

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