CIARA {CIARA}

CIARA

Description

It selects highly localized genes as specified in CIARA_gene, starting from genes in background

Usage

CIARA(
  norm_matrix,
  knn_matrix,
  background,
  cores_number = 1,
  p_value = 0.001,
  odds_ratio = 2,
  local_region = 1,
  approximation = FALSE
)

Arguments

norm_matrix

Norm count matrix (n_genes X n_cells).

knn_matrix

K-nearest neighbors matrix (n_cells X n_cells).

background

Vector of genes for which the function CIARA_gene is run.

cores_number

Integer.Number of cores to use.

p_value

p value returned by the function fisher.test with parameter alternative = "g"

odds_ratio

odds_ratio returned by the function fisher.test with parameter alternative = "g"

local_region

Integer. Minimum number of local regions (cell with its knn neighbours) where the binarized gene expression is enriched in 1.

approximation

Logical.For a given gene, the fisher test is run in the local regions of only the cells where the binarized gene expression is 1.

Value

Dataframe with n_rows equal to the length of background . Each row is the output from CIARA_gene.

Author(s)

Gabriele Lubatti [e-mail]