### R code from vignette source 'using_pcxn.Rnw' ################################################### ### code chunk number 1: queries ################################################### # Select a query gene set from a specific collection while requesting # the 10 most correlated neighbors, whether the correlation coefficients are # adjusted for gene overlap and specific cut-offs for minimum absolute # correlation and maximum p-value library(pcxn) library(pcxnData) data(list = c("pathprint.Hs.gs", "pathCor_pathprint_v1.2.3_dframe", "pathCor_pathprint_v1.2.3_unadjusted_dframe", "pathCor_CPv5.1_dframe", "gobp_gs_v5.1")) pcxn.obj <- pcxn_explore(collection = "pathprint", query_geneset = "Alzheimer's disease (KEGG)", adj_overlap = TRUE, top = 10, min_abs_corr = 0.05, max_pval = 0.05) # Select one or two pathway groups from a specific collection while requesting # the 10 most correlated neighbors, whether the correlation coefficients are # adjusted for gene overlap and specific cut-offs for minimum absolute # correlation and maximum p-value pcxn.obj <- pcxn_analyze("pathprint",c("ABC transporters (KEGG)", "ACE Inhibitor Pathway (Wikipathways)", "AR down reg. targets (Netpath)"), c("DNA Repair (Reactome)"), adj_overlap = FALSE, 10, 0.05, 0.05) ################################################### ### code chunk number 2: pcxn_gene_members ################################################### # Use the pcxn package to select pathway from any collection and get it's # gene members as a list gene_member_list <- pcxn_gene_members("Alzheimer's disease (KEGG)") ################################################### ### code chunk number 3: pcxn_heatmap ################################################### # Creare the pcxn object needed as an input pcxn.obj <- pcxn_analyze("pathprint",c("ABC transporters (KEGG)", "ACE Inhibitor Pathway (Wikipathways)", "AR down reg. targets (Netpath)"), c("DNA Repair (Reactome)"), 10, 0.05, 0.05) # Draw the heatmap heatmap <- pcxn_heatmap(pcxn.obj, "complete") ################################################### ### code chunk number 4: pcxn_network ################################################### # Create the pcxn object needed as an input pcxn.obj <- pcxn_analyze("pathprint",c("ABC transporters (KEGG)", "ACE Inhibitor Pathway (Wikipathways)", "AR down reg. targets (Netpath)"), c("DNA Repair (Reactome)"), 10, 0.05, 0.05) # Create the network # network <- pcxn_network(pcxn.obj)