specific_CCCScores_spots | R Documentation |
Specific Cell-Cell communication scores based on spatial expression of interacting cells at spots resulation
specific_CCCScores_spots(
gobject,
expr_residual,
dwls_values,
proximityMat,
random_iter = 1000,
cell_type_1 = "astrocytes",
cell_type_2 = "endothelial",
gene_set_1,
gene_set_2,
min_observations = 2,
detailed = FALSE,
adjust_method = c("fdr", "bonferroni", "BH", "holm", "hochberg", "hommel", "BY",
"none"),
adjust_target = c("genes", "cells"),
set_seed = FALSE,
seed_number = 1234,
verbose = T
)
gobject |
giotto object to use |
expr_residual |
spatial network to use for identifying interacting cells |
dwls_values |
dwls matrix |
proximityMat |
cell cell communication score matrix |
random_iter |
number of iterations |
cell_type_1 |
first cell type |
cell_type_2 |
second cell type |
gene_set_1 |
first specific gene set from gene pairs |
gene_set_2 |
second specific gene set from gene pairs |
min_observations |
minimum number of interactions needed to be considered |
detailed |
provide more detailed information (random variance and z-score) |
adjust_method |
which method to adjust p-values |
adjust_target |
adjust multiple hypotheses at the cell or gene level |
set_seed |
set a seed for reproducibility |
seed_number |
seed number |
verbose |
verbose |
Statistical framework to identify if pairs of genes (such as ligand-receptor combinations) are expressed at higher levels than expected based on a reshuffled null distribution of gene expression values in cells that are spatially in proximity to eachother.
LR_comb:Pair of ligand and receptor
lig_cell_type: cell type to assess expression level of ligand
lig_expr: average expressionresidual(observed - DWLS_predicted) of ligand in lig_cell_type
ligand: ligand name
rec_cell_type: cell type to assess expression level of receptor
rec_expr: average expression residual(observed - DWLS_predicted) of receptor in rec_cell_type
receptor: receptor name
LR_expr: combined average ligand and receptor expression
lig_nr: total number of cells from lig_cell_type that spatially interact with cells from rec_cell_type
rec_nr: total number of cells from rec_cell_type that spatially interact with cells from lig_cell_type
rand_expr: average combined ligand and receptor expression residual from random spatial permutations
av_diff: average difference between LR_expr and rand_expr over all random spatial permutations
sd_diff: (optional) standard deviation of the difference between LR_expr and rand_expr over all random spatial permutations
z_score: (optinal) z-score
log2fc: LR_expr - rand_expr
pvalue: p-value
LR_cell_comb: cell type pair combination
p.adj: adjusted p-value
PI: significanc score: log2fc * -log10(p.adj)
Cell-Cell communication scores for gene pairs based on spatial interaction
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.