findPure: Find pure cells

In lingxuez/SOUP: Semi-soft Clustering of Single Cell Data

Description

Find the list of pure cells with the highest purity scores.

Usage

findPure(A, ext.prop = NULL, pure.prop = 0.5)

Arguments

A	cell-by-cell similarity matrix.
ext.prop	(optional) the proportion of extreme neighbors for each cell, such that ext.prop*n.cells is roughly the number of pure cells per cluster. By default, ext.prop=0.1 for less than 1,000 cells, and ext.prop=0.05 for larger datasets.
pure.prop	(optional) the proportion of pure cells in the data. By default pure.prop=0.5.

Value

A list containing

i.pure

indices for the top pure.prop*n.cells pure cells.

purity

purity scores of all cells.

lingxuez/SOUP documentation built on May 28, 2019, 3:38 p.m.