compare_normal_emp_pvals: compare_normal_emp_pvals

In saeyslab/multinichenetr: MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

compare_normal_emp_pvals

Description

compare_normal_emp_pvals Compare nr and rank of DE genes between normal p-values and empirical p-values

Usage

compare_normal_emp_pvals(DE_info, DE_info_emp, adj_pval = FALSE)

Arguments

DE_info	Output of 'get_DE_info'
DE_info_emp	Output of 'get_empirical_pvals'
adj_pval	Should the adjusted p-values be compared (TRUE) or the non-adjusted ones (FALSE)? Defautl: FALSE

Value

a list òf plots for each celltype-contrast pair: an upset plot and line plot are drawn.

Examples

## Not run: 
library(dplyr)
sample_id = "tumor"
group_id = "pEMT"
celltype_id = "celltype"
batches = NA
covariates = NA
contrasts_oi = c("'High-Low','Low-High'")
senders_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique()
receivers_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique()
DE_info = get_DE_info(
   sce = sce,
   sample_id = sample_id,
   celltype_id = celltype_id,
   group_id = group_id,
   batches = batches,
   covariates = covariates,
   contrasts = contrasts_oi)
DE_info_emp = get_empirical_pvals(DE_info$celltype_de$de_output_tidy)
comparison_plots = compare_normal_emp_pvals(DE_info, DE_info_emp)

## End(Not run)

saeyslab/multinichenetr documentation built on Jan. 15, 2025, 7:55 p.m.