### First download and save the developing and adult human brain microarray data require(BrainGEP) ## save_path is the character vector specifying the path where the processed developing and adult brain data is stored Load_AHBA_data(save_path) ### Pairwise gene-gene correlations ### # Developing Epileptic encephalopathy reference gene-gene correlations with regional option AHBA_pairwise_gene_correlations("DHB",EE_ref_genes,"R") # Developing Epileptic encephalopathy reference gene-gene correlations without regional option AHBA_pairwise_gene_correlations("DHB",EE_ref_genes,"N") # Adult Epileptic encephalopathy reference gene-gene correlations with regional (cerebellum CB, cortex CX and brainstem BS) option AHBA_pairwise_gene_correlations("AHB",EE_ref_genes,"R") # Adult Epileptic encephalopathy reference gene-gene correlations without regional option AHBA_pairwise_gene_correlations("AHB",EE_ref_genes,"N") ### Heatmaps ### # Developing brain individual heatmaps across cortex (CX) and non-CX regions AHBA_heatmap("DHB",EE_ref_genes,"R") # Developing brain individual heatmaps across whole brain AHBA_heatmap("DHB",EE_ref_genes,"NA") # Adult brain individual heatmaps across cerebellum (CB), cortex (CX) and brainstem (BS) regions AHBA_heatmap("AHB",EE_ref_genes,"R") # Adult brain individual heatmaps across whole brain AHBA_heatmap("AHB",EE_ref_genes,"NA") ### Ref_genes ### AHBA_refgenes("DHB",EE_ref_genes,"pearson","R") AHBA_refgenes("AHB",EE_ref_genes,"pearson","R") AHBA_refgenes("DHB",EE_ref_genes,"pearson","N") AHBA_refgenes("AHB",EE_ref_genes,"pearson","N") ### ECDF curves ### # Developing Epileptic encephalopathy reference genes-gene correlations vs 1000 randomly chosen gene-gene correlations with regional option, Pearsons correlation AHBA_ECDF("DHB",EE_ref_genes,"pearson",unlist(random_gene_symbol_1000),"R") # Developing Epileptic encephalopathy reference genes-gene correlations vs 1000 randomly chosen gene-gene correlations without regional option, Pearsons correlation AHBA_ECDF("DHB",EE_ref_genes,"pearson",unlist(random_gene_symbol_1000),"N") # Adult Epileptic encephalopathy reference genes-gene correlations vs 1000 randomly chosen gene-gene correlations with regional option, Pearsons correlation AHBA_ECDF("AHB",EE_ref_genes,"pearson",unlist(random_gene_symbol_1000),"R") # Adult Epileptic encephalopathy reference genes-gene correlations vs 1000 randomly chosen gene-gene correlations without regional option, Pearsons correlation AHBA_ECDF("AHB",EE_ref_genes,"pearson",unlist(random_gene_symbol_1000),"N") ### Network ### # Adult Epileptic encephalopathy reference gene regional circular network, based on pre-calculated top 5% R value, Pearsons correlation AHBA_network("AHB",EE_ref_genes,"pearson","NA","R",AHB_Pearson_top_5p,"NA","circular") # Adult Epileptic encephalopathy reference gene whole-brain spring network, based on pre-calculated top 5% R value, Pearsons correlation AHBA_network("AHB",EE_ref_genes,"pearson","NA","NA",AHB_Pearson_top_5p,"NA","spring") # Developing Epileptic encephalopathy reference gene whole-brain circular network, based on pre-calculated top 5% R value, Pearsons correlation AHBA_network("DHB",EE_ref_genes,"pearson","NA","R",DHB_Pearson_top_5p,"NA","circular") # Developing Epileptic encephalopathy reference gene whole-brain circular network, based on pre-calculated top 5% R value, Pearsons correlation AHBA_network("DHB",EE_ref_genes,"pearson","NA","NA",DHB_Pearson_top_5p,"NA","circular") # Adult Epileptic encephalopathy reference gene whole-brain circular network, calculating the R value at which the top 5% connections are found, Pearsons correlation AHBA_network("AHB",EE_ref_genes,"pearson",0.95,"NA","NA","NA","circular") ### Corrplot ### # Developing Epileptic encephalopathy reference gene-gene correlation plot showing correlations across the whole brain AHBA_corrplot("DHB", EE_ref_genes, "spearman", "R") # Developing Epileptic encephalopathy reference gene-gene correlation plot showing correlations across CX and non-CX regions AHBA_corrplot("DHB", EE_ref_genes, "spearman", "N") # Adult Epileptic encephalopathy reference gene-gene correlation plot showing output by regions (CB, CX, BS), Pearsons correlation AHBA_corrplot("AHB", EE_ref_genes, "pearson", "R") # Adult Epileptic encephalopathy reference gene-gene correlation plot showing correlations across the whole brain, Pearsons correlation AHBA_corrplot("AHB", EE_ref_genes, "pearson", "N") ### Prioritisation ### # Prioritisation of EE candidate genes across whole developing brain, Pearsons correlation AHBA_Prioritise("DHB", EE_ref_genes, EE_cand_genes, "pearson", "NA", DHB_Pearson_top_5p,"R") # Prioritisation of EE candidate genes across whole adult brain, Pearsons correlation AHBA_Prioritise("AHB", EE_ref_genes, EE_cand_genes, "pearson", "NA", AHB_Pearson_top_5p,"N") # Prioritisation of EE candidate genes across regional adult brain, Pearsons correlation AHBA_Prioritise("AHB", EE_ref_genes, EE_cand_genes, "pearson", "NA", AHB_Pearson_top_5p,"R") # Prioritisation of EE candidate genes across whole developing brain, Pearsons correlation AHBA_Prioritise("DHB", EE_ref_genes, EE_cand_genes, "pearson", "NA", DHB_Pearson_top_5p,"N") # Prioritisation of EE candidate genes across CB, CX and BS regions in the adult brains, Spearmans correlation AHBA_Prioritise("AHB", EE_ref_genes, EE_cand_genes, "spearman", "NA", AHB_Spearman_top_5p,"R")