## ----eval=FALSE------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("CTDquerier") ## ----message=FALSE--------------------------------------------------------- library( CTDquerier ) ## ----args_query_gene------------------------------------------------------- args( query_ctd_gene ) ## ----ctd_genes------------------------------------------------------------- ctd_genes <- query_ctd_gene( terms = c( "APOE", "APOEB", "APOE2", "APOE3" , "APOE4", "APOA1", "APOA5" ) ) ctd_genes ## ----ctd_get_genes--------------------------------------------------------- get_terms( ctd_genes ) ## ----ctd_gene_ext_dise----------------------------------------------------- get_table( ctd_genes , index_name = "diseases" )[ 1:2, 1:3 ] ## ----ctd_gene_ext_tbl------------------------------------------------------ colnames( get_table( ctd_genes, index_name = "chemical interactions" ) ) colnames( get_table( ctd_genes, index_name = "diseases" ) ) colnames( get_table( ctd_genes, index_name = "gene-gene interactions" ) ) colnames( get_table( ctd_genes, index_name = "kegg pathways" ) ) colnames( get_table( ctd_genes, index_name = "go terms" ) ) ## ----ctd_gene_hm_chem------------------------------------------------------ plot( ctd_genes, index_name = "chemical interactions", filter.score = 3 ) ## ----ctd_gene_hm_dise------------------------------------------------------ plot( ctd_genes, index_name = "disease", filter.score = 115 ) ## ----ctd_gene_ntw_gene----------------------------------------------------- plot( ctd_genes, index_name = "gene-gene interactions", representation = "network", main = "APOE-like gene-gene interactions" ) ## ----ctd_gen_ntw_hegg------------------------------------------------------ plot( ctd_genes, index_name = "kegg pathways", representation = "network", main = "KEGG pathways related to APOE genes" ) ## ----ctd_gen_ntw_go-------------------------------------------------------- plot( ctd_genes, index_name = "go terms", representation = "network", main = "GO terms related to APOE genes", ontology = "Molecular Function" ) ## ----args_query_chem------------------------------------------------------- args( query_ctd_chem ) ## ----ctd_chem-------------------------------------------------------------- ctd_chem <- query_ctd_chem( terms = c( "Zinc", "Cadmium" ) ) ctd_chem ## ----ctd_get_chem---------------------------------------------------------- get_terms( ctd_chem ) ## ----ctd_chem_ext_dise----------------------------------------------------- get_table( ctd_chem , index_name = "diseases" )[ 1:2, 1:6 ] ## ----ctd_chem_ext_tbl------------------------------------------------------ colnames( get_table( ctd_chem, index_name = "gene interactions" ) ) colnames( get_table( ctd_chem, index_name = "diseases" ) ) colnames( get_table( ctd_chem, index_name = "kegg pathways" ) ) colnames( get_table( ctd_chem, index_name = "go terms" ) ) ## ----ctd_chem_hm_gene------------------------------------------------------ plot( ctd_chem, index_name = "gene interactions", filter.score = 5 ) ## ----ctd_chem_ntw_gene----------------------------------------------------- plot( ctd_chem, index_name = "gene interactions", representation = "network", filter.score = 3, main = "Gen-Chemical interaction for Zinc and Cadmium" ) ## ----ctd_chm_htm_dise------------------------------------------------------ plot( ctd_chem, index_name = "disease" ) ## ----ctd_chem_htm_kegg----------------------------------------------------- plot( ctd_chem, index_name = "kegg pathways", filter.score = 1e-40 ) ## ----ctd_chem_htm_go, fig.height=8----------------------------------------- plot( ctd_chem, index_name = "go terms", representation = "network", filter.score = 1e-210 ) ## ----args_query_dise------------------------------------------------------- args( query_ctd_dise ) ## ----ctd_dise-------------------------------------------------------------- ctd_diseases <- query_ctd_dise( terms = c( "Dementia", "Alzheimer" ) ) ctd_diseases ## ----ctd_get_dise---------------------------------------------------------- get_terms( ctd_diseases ) ## ----ctd_dise_ext_gene----------------------------------------------------- get_table( ctd_diseases , index_name = "gene interactions" )[ 1:2, 1:5 ] ## ----ctd_dise_ext_tbl------------------------------------------------------ colnames( get_table( ctd_diseases, index_name = "gene interactions" ) ) colnames( get_table( ctd_diseases, index_name = "chemical interactions" ) ) colnames( get_table( ctd_diseases, index_name = "kegg pathways" ) ) ## ----ctd_dise_htm_gen, fig.height=8---------------------------------------- plot( ctd_diseases, index_name = "gene interactions", filter.score = 75 ) ## ----ctd_dise_htm_chm------------------------------------------------------ plot( ctd_diseases, index_name = "chemical interactions", filter.score = 35 ) ## ----ctd_dise_ntw_kegg----------------------------------------------------- plot( ctd_diseases, index_name = "kegg pathways", representation = "network", subset.disease = "Dementia" ) ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()