## ---- eval = FALSE------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("goSTAG") ## ---- warning = FALSE, message = FALSE---------------------------------------- library("goSTAG") ## ----------------------------------------------------------------------------- data( goSTAG_example_gene_lists ) head( lapply( goSTAG_example_gene_lists, head ) ) ## ---- eval = FALSE------------------------------------------------------------ # gene_lists <- loadGeneLists( "gene_lists.gmt" ) ## ---- eval = FALSE------------------------------------------------------------ # gene_lists <- loadGeneLists( "/gene/lists/directory", type = "DIR" ) ## ---- eval = FALSE------------------------------------------------------------ # gene_lists <- loadGeneLists( "/gene/lists/directory", type = "DIR", header = TRUE, col = 7 ) ## ---- warning = FALSE, message = FALSE---------------------------------------- go_terms <- loadGOTerms() head( lapply( go_terms, head ) ) head( go_terms[["ALL"]] ) ## ---- eval = FALSE------------------------------------------------------------ # go_terms <- loadGOTerms( use_archived = FALSE ) ## ----------------------------------------------------------------------------- go_terms_mouse <- loadGOTerms( species = "mouse", domain = "MF", min_num_genes = 10 ) ## ----------------------------------------------------------------------------- enrichment_matrix <- performGOEnrichment( goSTAG_example_gene_lists, go_terms ) head(enrichment_matrix) ## ---- eval = FALSE------------------------------------------------------------ # enrichment_matrix_FDR <- performGOEnrichment( goSTAG_example_gene_lists, go_terms, filter_method = "p.adjust", significance_threshold = 0.3, p.adjust_method = "BH" ) ## ----------------------------------------------------------------------------- hclust_results <- performHierarchicalClustering( enrichment_matrix ) hclust_results ## ----------------------------------------------------------------------------- hclust_results_euclidean <- performHierarchicalClustering( enrichment_matrix, distance_method = "euclidean", clustering_method = "complete" ) ## ----------------------------------------------------------------------------- sample_hclust_results <- performHierarchicalClustering( enrichment_matrix, feature = "col" ) ## ----------------------------------------------------------------------------- clusters <- groupClusters( hclust_results_euclidean ) lapply( head( clusters ), head ) ## ----------------------------------------------------------------------------- length( clusters ) ## ----------------------------------------------------------------------------- clusters_larger_threshold <- groupClusters( hclust_results_euclidean, distance_threshold = 0.5 ) length( clusters_larger_threshold ) ## ----------------------------------------------------------------------------- clusters_smaller_threshold <- groupClusters( hclust_results_euclidean, distance_threshold = 0.05 ) length( clusters_smaller_threshold ) ## ----------------------------------------------------------------------------- cluster_labels <- annotateClusters( clusters ) head( cluster_labels ) ## ----------------------------------------------------------------------------- plotHeatmap( enrichment_matrix, hclust_results_euclidean, clusters, cluster_labels ) ## ----------------------------------------------------------------------------- plotHeatmap( enrichment_matrix, hclust_results_euclidean, clusters, cluster_labels, sample_hclust_results = sample_hclust_results ) ## ----------------------------------------------------------------------------- plotHeatmap( enrichment_matrix, hclust_results_euclidean, clusters, cluster_labels, min_num_terms = 5 ) ## ---- eval = FALSE------------------------------------------------------------ # png( "heatmap.png", width = 1600, height = 1200 ) # plotHeatmap( enrichment_matrix, hclust_results_euclidean, clusters, cluster_labels, dendrogram_lwd = 2, header_lwd = 2, cluster_label_cex = 2, sample_label_cex = 2 ) # dev.off() ## ----------------------------------------------------------------------------- citation("goSTAG") ## ----------------------------------------------------------------------------- sessionInfo()