csangara
commented
9 months ago You cannot set the gene set of interest as the same as the background. NicheNet looks for the enrichment of the gene set of interest within the background, so setting these two as the same does not make sense.
I followed this workflow so far: `organism <- "human" lr_network <- readRDS(url("https://zenodo.org/record/7074291/files/lr_network_human_21122021.rds")) ligand_target_matrix <- readRDS(url("https://zenodo.org/record/7074291/files/ligand_target_matrix_nsga2r_final.rds"))
fibroblast_clusters <- c('1', '2', '3') malignant_clusters <- c('1', '2', '3') fibroblast_cells <- obj@assays$SCT@counts[, obj@meta.data$fibroblast_clusters %in% fibroblast_clusters] malignant_cells <- obj@assays$SCT@counts[, obj@meta.data$malignant_clusters %in% malignant_clusters] geneset_oi <- rownames(malignant_cells)[rowSums(malignant_cells != 0) > 0] ligands <- lr_network %>% dplyr::pull(from) %>% unique() expressed_ligands <- intersect(ligands, rownames(fibroblast_cells)) receptors <- lr_network %>% dplyr::pull(to) %>% unique() expressed_receptors <- intersect(receptors, rownames(malignant_cells)) lr_network_expressed <- lr_network %>% filter(from %in% expressed_ligands & to %in% expressed_receptors) potential_ligands <- lr_network_expressed %>% dplyr::pull(from) %>% unique()
ligand_activities <- predict_ligand_activities( geneset = geneset_oi, background_expressed_genes = geneset_oi, # You can use the same gene set for background ligand_target_matrix = ligand_target_matrix, potential_ligands = potential_ligands )`
But I got this error: `> ligand_activities <- predict_ligand_activities(
What do you think about the problem?
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Edmonton tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 purrr_1.0.2
[5] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 tidyverse_2.0.0
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[29] sp_2.0-0 Matrix_1.6-1 Giotto_1.1.2
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