getDAregion: DA-seq Step 3: get DA regions

In JunZhao1990/DAseq: Detecting regions of differential abundance between scRNA-seq datasets

Description

Cluster the DA cells retained from Step 1 and Step 2 of DA-seq with outlier removal to obtain spatially coherent DA regions.

Usage

getDAregion(X, cell.idx, k, alpha, restr.fact = 50, cell.labels,
  labels.1, labels.2, do.plot = T, plot.embedding = NULL, size = 0.5,
  seed = 0, ...)

Arguments

X	size N-by-p matrix, input merged dataset of interest after dimension reduction
cell.idx	result "da.cell.idx" from the output of function getDAcells
k	number of DA regions to find for cells from function getDAcells
alpha	estimated ratio of outliers of cells from function getDAcells
restr.fact	parameter inherited from function "tclust"
cell.labels	size N vector, labels for each input cell
labels.1	vector, label name(s) that represent condition 1
labels.2	vector, label name(s) that represent condition 2
do.plot	a logical value to indicate whether to return ggplot objects showing the results, default True
plot.embedding	size N-by-2 matrix, 2D embedding for the cells
size	cell size to use in the plot, default 0.5
...	other parameters passed to function tclust

Value

a list of results

cluster.res

DA region number for each cell from cell.idx, '0' represents outlier cells

DA.stat

a table showing DA score and p-value for each DA region

da.region.plot

ggplot object showing DA regions on plot.embedding

JunZhao1990/DAseq documentation built on April 30, 2020, 10:10 a.m.