【miloR】differential abundance testing

library(miloR)
library(SingleCellExperiment)
library(scater)
library(scran)
library(dplyr)
library(patchwork)

miloR的使用场景：两个或多个condition，每个condition都有生物学重复。主要分为三步：

1. Sampling of representative neighbourhoods
2. Testing for differential abundance of conditions in all neighbourhoods
3. Accounting for multiple hypothesis testing using a weighted FDR procedure that accounts for the overlap of neighbourhoods

对workflow的基本描述：

1，数据预处理与降维

2，minimizing batch effects.如harmony等整合多sample的算法，但不要使用conos

3，building the KNN graph

4，definition of cell neighbourhoods and index cell samplling 

5，testing for differencial abundance in neighbourhoods

选择参数的建议：

K值过小时每个neigubourhood的细胞数可能过少，以至于不能进行组间DA差异

建议K >= samples X3~5

但是如果K值选的过大，每个neighbou