DIALOGUE_make.cell.type.seurat: DIALOGUE_make.cell.type.seurat

In livnatje/DIALOGUE: DIALOGUE is a dimensionality reduction algorithm that uses cross-cell-type associations to identify multicellular programs and map the cell transcriptome as a function of its environment.

DIALOGUE_make.cell.type.seurat

Description

Using Seurat objects as input for DIALOGUE make.cell.type function

Usage

DIALOGUE_make.cell.type.seurat(obj, cell.subtypes, name)

Arguments

obj	Seurat object
cell.subtypes	the cell type or subtype to be use. Make sure the obj metadata includes a column of "cell.subtypes"
name	the name to be used in the DIALOGUE run to refer to this cell type.

Examples

# Run DIALOGUE with simulated PBMC data
r1<-DIALOGUE_make.cell.type.seurat(obj, cell.subtypes = "CD8.T.cell", name = "CD8.T.cell")
r1<- DIALOGUE_make.cell.type.seurat(obj, cell.subtypes = c("Naive CD4 T","Memory CD4 T","CD8 T"), name = "T.cell")
r2<- DIALOGUE_make.cell.type.seurat(obj, cell.subtypes = c("CD14+ Mono","FCGR3A+ Mono","DC"), name = "Myeloid")
rA<- list(A = r1,B = r2)
R <- DIALOGUE.run(rA = rA, main = "ToyExample",k = 2, results.dir = "DIALOGUE.output",spatial.flag = F,plot.flag = T,conf = "cellQ")

livnatje/DIALOGUE documentation built on Jan. 30, 2024, 1:31 a.m.