Identify over-expressed signaling genes associated with each cell group
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
)CellChat object
a customed data matrix. Default: data.use = NULL and the expression matrix in the slot 'data.signaling' is used
cell group information; default is `object@idents`; otherwise it should be one of the column names of the meta slot
a subset of cell groups used for analysis
whether invert the idents.use
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
the dataset name used for identifying highly enriched genes in this dataset for each cell group
a char name used for storing the over-expressed signaling genes in `object@var.features[[features.name]]`
Only return positive markers
features used for identifying Over Expressed genes. default use all features
whether return the object; otherwise return a data frame consisting of over-expressed signaling genes associated with each cell group
Threshold of the percent of cells expressed in one cluster
Threshold of Log Fold Change
Threshold of p-values
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 `object@var.features` `object@var.features[[features.name]]` is a vector consisting of the identified over-expressed signaling genes; `object@var.features[[paste0(features.name, ".info")]]` is a data frame returned from the differential expression analysis