SignacX (version 2.2.5)

CID.smooth: Smoothing function

Description

CID.smooth uses k-nearest neighbors to identify cells which correspond to a different label than the majority of their first-degree neighbors. If so, those annotations are "smoothed."

Usage

CID.smooth(ac, dM)

Arguments

ac

list containing a character vector where each element is a cell type or cell state assignment.

dM

distance matrix (see ?CID.GetDistMat).

Value

A character vector with smoothed labels

Examples

# NOT RUN {
# load data classified previously (see SignacFast)
P <- readRDS("celltypes.rds")
S <- readRDS("pbmcs.rds")

# get edges from default assay from Seurat object
default.assay <- Seurat::DefaultAssay(S)
edges = S@graphs[[which(grepl(paste0(default.assay, "_nn"), names(S@graphs)))]]

# get distance matrix
D = CID.GetDistMat(edges)

# smooth labels
smoothed = CID.smooth(ac = P$CellTypes, dM = D[[1]])
# }