check_gene_filter1: Check the first filtering step.

In wikiselev/clustools: Tools for cluster analysis of single cell high throughput data

Description

Evaluate Adjusted Rand index based on gene_filter1() parameters. NOTE that gene_filter2 is set to "none", distance is set to "spearman" and transformation is set to "spectral". These parameters were chosen because they provide the best clustering index.

Usage

check_gene_filter1(d, min.cells, max.cells, min.reads, n.dim)

Arguments

d	Expression matrix with rows as genes and columns as cells. Column names of d should represent the ground truth clustering indecies.
min.cells	Minimum number of cells in which a given gene is expressed.
max.cells	Maximum number of cells in which a given gene is expressed.
min.reads	Minimum number of reads per gene per cell.
n.dim	Number of dimension of the transformed distance matrix which is used in kmeans clustering.

Value

Adjusted Rand index of the clustering.

Examples

check_gene_filter1(quake, 3, 3, 2, 4)

wikiselev/clustools documentation built on May 4, 2019, 5:25 a.m.