## ----first_load, echo=TRUE, warning=FALSE, results='hide', message=FALSE------ library(RITANdata) library(RITAN) library(knitr) kable( attr(network_list, 'network_data_sources') ) kable( sapply(geneset_list, length), col.names = c('# Genesets') ) ## ----geneset_overlap_P, echo=TRUE, eval=FALSE, warning=FALSE, fig.width = 7, fig.height = 7, fig.align='center'---- # genes <- geneset_list$MSigDB_C5$APICAL_JUNCTION_COMPLEX # e <- network_overlap( genes, resources = c('CCSB','STRING'), minStringScore = 700 ) # ## We also strongly encourage use of the BioPlex database, which we do not distribute with RITAN in compliance with their licensing. ## ----geneset_overlap_M, echo=TRUE, eval=FALSE, warning=FALSE, fig.width = 7, fig.height = 7, fig.align='center'---- # genes2 <- geneset_list$MSigDB_C5$AMINE_METABOLIC_PROCESS # e2 <- network_overlap( genes, resources = c('PID','HumanNet') ) ## ----geneset_overlap_E, echo=TRUE, eval=FALSE, warning=FALSE, fig.width = 7, fig.height = 7, fig.align='center'---- # genes2 <- geneset_list$MSigDB_C5$AMINE_METABOLIC_PROCESS # e2 <- network_overlap( genes, resources = c('ChEA','HumanNet') )