test_hvg: test_hvg

In CIARA: Cluster Independent Algorithm for Rare Cell Types Identification

test_hvg

Description

For each cluster in cluster, HVGs are defined with Seurat function FindVariableFeatures. A Fisher test is performed to see if there is a statistically significant enrichment between the top number_hvg and the localized_genes

Usage

test_hvg(
  raw_counts,
  cluster,
  localized_genes,
  background,
  number_hvg,
  min_p_value
)

Arguments

raw_counts	Raw count matrix (n_genes X n_cells).
cluster	Vector of length equal to the number of cells, with cluster assignment.
localized_genes	Character vector with localized genes detected by CIARA.
background	Character vector with all the genes names to use as background for the Fisher test.
number_hvg	Integer value. Number of top HVGs provided by the Seurat function FindVariableFeatures.
min_p_value	Threshold on p values provided by Fisher test.

Value

A list with two elements.

first element	The first one is a list with length equal to the number of clusters. Each entry is list of three elements. The first two elements contain the p value and the odds ration given by the Fisher test The third is a vector with genes names that are present both in localized_genes and in top number_hvg HVGs .
second element	a character vector with the name of the cluster that have a p value smaller than min_p_value.

Author(s)

Gabriele Lubatti [e-mail]

See Also

https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/fisher.test

CIARA documentation built on March 18, 2022, 6:48 p.m.