Overlap modules with TF target genes
Examples
OverlapModulesDEGs
#> function (seurat_obj, deg_df, fc_cutoff = 0.5, group_col = "cluster",
#> wgcna_name = NULL, ...)
#> {
#> if (is.null(wgcna_name)) {
#> wgcna_name <- seurat_obj@misc$active_wgcna
#> }
#> deg_df$group <- deg_df[, group_col]
#> cell_groups <- deg_df$group %>% unique
#> modules <- GetModules(seurat_obj)
#> mods <- levels(modules$module)
#> mods <- mods[mods != "grey"]
#> if (fc_cutoff >= 0) {
#> deg_df <- subset(deg_df, avg_log2FC >= fc_cutoff)
#> }
#> else {
#> deg_df <- subset(deg_df, avg_log2FC <= fc_cutoff)
#> deg_df$avg_log2FC <- -1 * deg_df$avg_log2FC
#> fc_cutoff <- -1 * fc_cutoff
#> }
#> genome.size <- nrow(seurat_obj)
#> overlap_df <- do.call(rbind, lapply(mods, function(cur_mod) {
#> cur_module_genes <- modules %>% subset(module == cur_mod) %>%
#> .$gene_name
#> cur_overlap_df <- do.call(rbind, lapply(cell_groups,
#> function(cur_group) {
#> cur_DEGs <- deg_df %>% subset(group == cur_group &
#> p_val_adj <= 0.05 & avg_log2FC > fc_cutoff) %>%
#> .$gene
#> cur_overlap <- testGeneOverlap(newGeneOverlap(cur_module_genes,
#> cur_DEGs, genome.size = genome.size))
#> c(cur_overlap@odds.ratio, cur_overlap@pval, cur_overlap@Jaccard,
#> length(cur_overlap@intersection))
#> })) %>% as.data.frame
#> colnames(cur_overlap_df) <- c("odds_ratio", "pval", "Jaccard",
#> "size_intersection")
#> cur_overlap_df$module <- cur_mod
#> cur_overlap_df$group <- cell_groups
#> cur_overlap_df$color <- modules %>% subset(module ==
#> cur_mod) %>% .$color %>% unique
#> cur_overlap_df
#> }))
#> overlap_df$fdr <- p.adjust(overlap_df$pval, method = "fdr")
#> overlap_df$Significance <- gtools::stars.pval(overlap_df$fdr)
#> overlap_df$Significance <- ifelse(overlap_df$Significance ==
#> ".", "", overlap_df$Significance)
#> overlap_df$module <- factor(overlap_df$module, levels = mods)
#> overlap_df <- overlap_df %>% dplyr::select(c(module, group,
#> color, odds_ratio, pval, fdr, Significance, Jaccard,
#> size_intersection))
#> overlap_df
#> }
#> <bytecode: 0x7f9614363708>
#> <environment: namespace:hdWGCNA>