updateDAcells: Update DA cells

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

Description

Use different threshold to select DA cells based on an output from getDAcells().

Usage

updateDAcells(X, pred.thres = NULL, force.thres = F, alpha = NULL,
  k.folds = 10, n.runs = 10, cell.labels = NULL, labels.1 = NULL,
  labels.2 = NULL, do.plot = T, plot.embedding = NULL, size = 0.5)

Arguments

X	output from getDAcells()
pred.thres	length-2 vector, top and bottom threshold on DA measure, default NULL, select significant DA cells based on permutation
force.thres	a logical value to indicate whether to forcefully use pred.thres without considering significance, default False
alpha	set this parameter to not NULL to rerun Logistic regression
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

Value

a list of results with updated DA cells

KlugerLab/DAseq documentation built on April 13, 2021, 9:02 p.m.