binSpectMultiMatrix: binSpectMultiMatrix

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

binSpectMultiMatrix

Description

binSpect for a single spatial network and a provided expression matrix

Usage

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 = T,
  knn_params = NULL,
  set.seed = NULL,
  summarize = c("adj.p.value", "p.value")
)

Arguments

expression_matrix	expression matrix
spatial_networks	list of spatial networks in data.table format
bin_method	method to binarize gene expression
subset_feats	only select a subset of features to test
kmeans_algo	kmeans algorithm to use (kmeans, kmeans_arma, kmeans_arma_subset)
nstart	kmeans: nstart parameter
iter_max	kmeans: iter.max parameter
extreme_nr	number of top and bottom cells (see details)
sample_nr	total number of cells to sample (see details)
percentage_rank	vector of percentages of top cells for binarization
do_fisher_test	perform fisher test
adjust_method	p-value adjusted method to use (see p.adjust)
calc_hub	calculate the number of hub cells
hub_min_int	minimum number of cell-cell interactions for a hub cell
get_av_expr	calculate the average expression per gene of the high expressing cells
get_high_expr	calculate the number of high expressing cells per gene
implementation	enrichment implementation (data.table, simple, matrix)
group_size	number of genes to process together with data.table implementation (default = automatic)
do_parallel	run calculations in parallel with mclapply
cores	number of cores to use if do_parallel = TRUE
verbose	be verbose
knn_params	list of parameters to create spatial kNN network
set.seed	set a seed before kmeans binarization
summarize	summarize the p-values or adjusted p-values

Value

data.table with results

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.