make_lite_output_condition_specific: make_lite_output_condition_specific

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

make_lite_output_condition_specific

Description

make_lite_output_condition_specific Reduce the size of the MultiNicheNet output object (for memory efficiency), by only keeping expression information for present ligands, receptors, and genes DE in at least one probed condition. This function is specific for an object that contains the prioritization tables of the condition-specific cell type workflow as well.

Usage

make_lite_output_condition_specific(multinichenet_output, top_n_LR = 2500)

Arguments

multinichenet_output	Output of a MultiNicheNet analysis (result of 'multi_nichenet_analysis()').
top_n_LR	top nr of LR pairs for which correlation with target genes will be calculated. Is 2500 by default. If you want to calculate correlation for all LR pairs, set this argument to NA.

Value

multinichenet output list (= result of 'multi_nichenet_analysis()'), but now filtered such that expression information is only returned for present ligands, receptors, and genes DE in at least one probed condition.

Examples

## Not run: 
library(dplyr)
multinichenet_output = multinichenet_output %>% make_lite_output_condition_specific()


## End(Not run)

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