identifyOverExpressedGenes: Identify over-expressed signaling genes associated with each...

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

Identify over-expressed signaling genes associated with each cell group

Description

USERS can use customized gene set as over-expressed signaling genes by setting '[e-mail][[features.name]] <- features.sig' The Bonferroni corrected/adjusted p value can be obtained via '[e-mail][[paste0(features.name, ".info")]]'. Note that by default 'features.name = "features"'

Usage

identifyOverExpressedGenes(
  object,
  data.use = NULL,
  group.by = NULL,
  idents.use = NULL,
  invert = FALSE,
  group.dataset = NULL,
  pos.dataset = NULL,
  features.name = "features",
  only.pos = TRUE,
  features = NULL,
  return.object = TRUE,
  thresh.pc = 0,
  thresh.fc = 0,
  thresh.p = 0.05
)

Arguments

object	CellChat object
data.use	a customed data matrix. Default: data.use = NULL and the expression matrix in the slot 'data.signaling' is used
group.by	cell group information; default is 'object@idents'; otherwise it should be one of the column names of the meta slot
idents.use	a subset of cell groups used for analysis
invert	whether invert the idents.use
group.dataset	dataset origin information in a merged CellChat object; set it as one of the column names of meta slot when identifying the highly enriched genes in one dataset for each cell group
pos.dataset	the dataset name used for identifying highly enriched genes in this dataset for each cell group
features.name	a char name used for storing the over-expressed signaling genes in '[e-mail][[features.name]]'
only.pos	Only return positive markers
features	features used for identifying Over Expressed genes. default use all features
return.object	whether return the object; otherwise return a data frame consisting of over-expressed signaling genes associated with each cell group
thresh.pc	Threshold of the percent of cells expressed in one cluster
thresh.fc	Threshold of Log Fold Change
thresh.p	Threshold of p-values

Value

A CellChat object or a data frame. If returning a CellChat object, two new elements named 'features.name' and paste0(features.name, ".info") will be added into the list '[e-mail]' '[e-mail][[features.name]]' is a vector consisting of the identified over-expressed signaling genes; '[e-mail][[paste0(features.name, ".info")]]' is a data frame returned from the differential expression analysis

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