## ----intro-------------------------------------------------------------------- library(ExperimentHub) eh <- ExperimentHub() eh <- query(eh, "LRcellTypeMarkers") eh ## show entries of LRcellTypeMarkers package ## ----extract_data------------------------------------------------------------- mouse_FC <- eh[['EH4548']] mouse_FC[1:6, 1:6] # show head of the data ## ----sort--------------------------------------------------------------------- library(LRcell) FC_marker_genes <- get_markergenes(mouse_FC, method="LR", topn=100) head(lapply(FC_marker_genes, head)) # glance at the marker genes ## ----load_example------------------------------------------------------------- library(LRcell) data("example_gene_pvals") head(example_gene_pvals, n=5) ## ----run_LRcell--------------------------------------------------------------- res <- LRcellCore(gene.p = example_gene_pvals, marker.g = FC_marker_genes, method = "LR", min.size = 5, sig.cutoff = 0.05) ## curate cell types res$cell_type <- unlist(lapply(strsplit(res$ID, '\\.'), '[', 2)) head(subset(res, select=-lead_genes)) ## ----plot_LRcellCore, fig.width=10, fig.height=6, dpi=120--------------------- plot_manhattan_enrich(res, sig.cutoff = .05, label.topn = 5) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()