check_gene_filter1: Check the first filtering step.

Description Usage Arguments Value Examples

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

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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

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