binSpect for a single spatial network and a provided expression matrix
binSpectMultiMatrix(
expression_matrix,
spatial_networks,
bin_method = c("kmeans", "rank"),
subset_feats = NULL,
kmeans_algo = c("kmeans", "kmeans_arma", "kmeans_arma_subset"),
nstart = 3,
iter_max = 10,
extreme_nr = 50,
sample_nr = 50,
percentage_rank = c(10, 30),
do_fisher_test = TRUE,
adjust_method = "fdr",
calc_hub = FALSE,
hub_min_int = 3,
get_av_expr = TRUE,
get_high_expr = TRUE,
implementation = c("data.table", "simple", "matrix"),
group_size = "automatic",
do_parallel = TRUE,
cores = NA,
verbose = TRUE,
knn_params = NULL,
set.seed = deprecated(),
seed = 1234,
summarize = c("adj.p.value", "p.value")
)expression matrix
list of spatial networks in data.table format
method to binarize gene expression
only select a subset of features to test
kmeans algorithm to use (kmeans, kmeans_arma, kmeans_arma_subset)
kmeans: nstart parameter
kmeans: iter.max parameter
number of top and bottom cells (see details)
total number of cells to sample (see details)
vector of percentages of top cells for binarization
perform fisher test
p-value adjusted method to use
(see p.adjust)
calculate the number of hub cells
minimum number of cell-cell interactions for a hub cell
calculate the average expression per gene of the high expressing cells
calculate the number of high expressing cells per gene
enrichment implementation (data.table, simple, matrix)
number of genes to process together with data.table implementation (default = automatic)
run calculations in parallel with mclapply
number of cores to use if do_parallel = TRUE
be verbose
list of parameters to create spatial kNN network
deprecated
sets value as seed before kmeans binarization. If NULL, no seed is set.
summarize the p-values or adjusted p-values
data.table with results