Compute the communication probability/strength between any interacting cell groups
computeCommunProb(
object,
type = c("triMean", "truncatedMean", "median"),
trim = NULL,
LR.use = NULL,
raw.use = FALSE,
population.size = FALSE,
nboot = 100,
seed.use = 1L,
Kh = 0.5,
n = 1
)CellChat object
methods for computing the average gene expression per cell group. By default = "triMean", producing fewer but stronger interactions; When setting `type = "truncatedMean"`, a value should be assigned to 'trim', producing more interactions.
the fraction (0 to 0.25) of observations to be trimmed from each end of x before the mean is computed
a subset of ligand-receptor interactions used in inferring communication network
whether use the raw data or the projected data. Set raw.use = FALSE to use the projected data when analyzing single-cell data with shallow sequencing depth because the projected data could help to reduce the dropout effects of signaling genes, in particular for possible zero expression of subunits of ligands/receptors. Set raw.use = TRUE when analyzing high-quality data
whether consider the proportion of cells in each group across all sequenced cells. Set population.size = FALSE if analyzing sorting-enriched single cells, to remove the potential artifact of population size. Set population.size = TRUE if analyzing unsorted single-cell transcriptomes, with the reason that abundant cell populations tend to send collectively stronger signals than the rare cell populations.
threshold of p-values
set a random seed. By default, set the seed to 1.
parameter in Hill function
parameter in Hill function
A CellChat object with updated slot 'net':
object@net$prob is the inferred communication probability (strength) array, where the first, second and third dimensions represent a source, target and ligand-receptor pair, respectively. USER can access all the inferred cell-cell communications using the function 'subsetCommunication(object)', which returns a data frame.
object@net$pval is the corresponding p-values of each interaction