test_hvg {CIARA} | R Documentation |
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 gabriele.lubatti@helmholtz-muenchen.de
See Also
https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/fisher.test