CIARA {CIARA} | R Documentation |
It selects highly localized genes as specified in CIARA_gene, starting from genes in background
CIARA(
norm_matrix,
knn_matrix,
background,
cores_number = 1,
p_value = 0.001,
odds_ratio = 2,
local_region = 1,
approximation = FALSE
)
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. |
Dataframe with n_rows equal to the length of background . Each row is the output from CIARA_gene.
Gabriele Lubatti gabriele.lubatti@helmholtz-muenchen.de