## ----warning=FALSE, message=FALSE, results='hide'----------------------------- library(FELLA) library(org.Mm.eg.db) library(KEGGREST) library(igraph) library(magrittr) set.seed(1) # Filter overview pathways graph <- buildGraphFromKEGGREST( organism = "mmu", filter.path = c("01100", "01200", "01210", "01212", "01230")) tmpdir <- paste0(tempdir(), "/my_database") # Mke sure the database does not exist from a former vignette build # Otherwise the vignette will rise an error # because FELLA will not overwrite an existing database unlink(tmpdir, recursive = TRUE) buildDataFromGraph( keggdata.graph = graph, databaseDir = tmpdir, internalDir = FALSE, matrices = "none", normality = "diffusion", niter = 100) ## ----warning=FALSE, message=FALSE, results='hide'----------------------------- alias2entrez <- as.list(org.Mm.eg.db::org.Mm.egSYMBOL2EG) entrez2ec <- KEGGREST::keggLink("enzyme", "mmu") entrez2path <- KEGGREST::keggLink("pathway", "mmu") fella.data <- loadKEGGdata( databaseDir = tmpdir, internalDir = FALSE, loadMatrix = "none" ) ## ----------------------------------------------------------------------------- fella.data ## ----------------------------------------------------------------------------- id.cpd <- getCom(fella.data, level = 5, format = "id") %>% names id.rx <- getCom(fella.data, level = 4, format = "id") %>% names id.ec <- getCom(fella.data, level = 3, format = "id") %>% names ## ----------------------------------------------------------------------------- cpd.nafld <- c( "C00020", # AMP "C00719", # Betaine "C00114", # Choline "C00037", # Glycine "C00160", # Glycolate "C01104" # Trimethylamine-N-oxide ) analysis.nafld <- enrich( compounds = cpd.nafld, data = fella.data, method = "diffusion", approx = "normality") ## ----------------------------------------------------------------------------- analysis.nafld %>% getInput %>% getName(data = fella.data) ## ----------------------------------------------------------------------------- getExcluded(analysis.nafld) ## ----fig.width=8, fig.height=8------------------------------------------------ plot( analysis.nafld, method = "diffusion", data = fella.data, nlimit = 250, plotLegend = FALSE) ## ----------------------------------------------------------------------------- g.nafld <- generateResultsGraph( object = analysis.nafld, data = fella.data, method = "diffusion") pscores.nafld <- getPscores( object = analysis.nafld, method = "diffusion") ## ----------------------------------------------------------------------------- cpd.nafld.suggestive <- c( "C00008", # ADP "C00791", # Creatinine "C00025", # Glutamate "C01026", # N,N-dimethylglycine "C00079", # Phenylalanine "C00299" # Uridine ) getName(cpd.nafld.suggestive, data = fella.data) ## ----------------------------------------------------------------------------- V(g.nafld)$name %>% intersect(cpd.nafld.suggestive) %>% getName(data = fella.data) ## ----------------------------------------------------------------------------- cpd.new.fig6 <- c( "C00101", # THF "C00440", # 5-CH3-THF "C00143", # 5,10-CH3-THF "C00073", # Methionine "C00019", # SAM "C00021", # SAH "C00155", # Homocysteine "C02291", # Cystathione "C00097" # Cysteine ) getName(cpd.new.fig6, data = fella.data) ## ----------------------------------------------------------------------------- cpd.new.fig6 %in% V(g.nafld)$name ## ----------------------------------------------------------------------------- wilcox.test( x = pscores.nafld[cpd.new.fig6], # metabolites from fig6 y = pscores.nafld[setdiff(id.cpd, cpd.new.fig6)], # rest of metabolites alternative = "less") ## ----------------------------------------------------------------------------- ec.cbs <- entrez2ec[[paste0("mmu:", alias2entrez[["Cbs"]])]] %>% gsub(pattern = "ec:", replacement = "") getName(fella.data, ec.cbs) ## ----------------------------------------------------------------------------- rx.cbs <- "R01290" getName(fella.data, rx.cbs) ## ----------------------------------------------------------------------------- c(rx.cbs, ec.cbs) %in% V(g.nafld)$name ## ----------------------------------------------------------------------------- # enzyme pscores.nafld[ec.cbs] mean(pscores.nafld[id.ec] <= pscores.nafld[ec.cbs]) # reaction pscores.nafld[rx.cbs] mean(pscores.nafld[id.rx] <= pscores.nafld[rx.cbs]) ## ----------------------------------------------------------------------------- ec.bhmt <- entrez2ec[[paste0("mmu:", alias2entrez[["Bhmt"]])]] %>% gsub(pattern = "ec:", replacement = "") getName(fella.data, ec.bhmt) ## ----------------------------------------------------------------------------- ec.bhmt %in% V(g.nafld)$name "R02821" %in% V(g.nafld)$name ## ----------------------------------------------------------------------------- entrez.slc22a5 <- alias2entrez[["Slc22a5"]] entrez.slc22a5 %in% names(entrez2ec) ## ----------------------------------------------------------------------------- path.slc22a5 <- entrez2path[paste0("mmu:", entrez.slc22a5)] %>% gsub(pattern = "path:", replacement = "") getName(fella.data, path.slc22a5) ## ----------------------------------------------------------------------------- path.slc22a5 %in% V(g.nafld)$name ## ----------------------------------------------------------------------------- symbol.fig3 <- c( "Cd36", "Scd2", "Apoa4", "Lcn2", "Apom") entrez.fig3 <- alias2entrez[symbol.fig3] %>% unlist %>% unique ec.fig3 <- entrez2ec[paste0("mmu:", entrez.fig3)] %T>% print %>% unlist %>% unique %>% na.omit %>% gsub(pattern = "ec:", replacement = "") getName(fella.data, ec.fig3) ## ----------------------------------------------------------------------------- ec.fig3 %in% V(g.nafld)$name ## ----------------------------------------------------------------------------- pscores.nafld[ec.fig3] mean(pscores.nafld[id.ec] <= pscores.nafld[ec.fig3]) ## ----------------------------------------------------------------------------- symbol.tableS2 <- c( "Mat1a", "Ahcyl2", "Cbs", "Mat2b", "Mtr") entrez.tableS2 <- alias2entrez[symbol.tableS2] %>% unlist %>% unique ec.tableS2 <- entrez2ec[paste0("mmu:", entrez.tableS2)] %T>% print %>% unlist %>% unique %>% na.omit %>% gsub(pattern = "ec:", replacement = "") ## ----------------------------------------------------------------------------- ec.tableS2 %in% V(g.nafld)$name ## ----------------------------------------------------------------------------- wilcox.test( x = pscores.nafld[ec.tableS2], # enzymes from table S2 y = pscores.nafld[setdiff(id.ec, ec.tableS2)], # rest of enzymes alternative = "less") ## ----------------------------------------------------------------------------- sessionInfo() ## ----------------------------------------------------------------------------- cat(getInfo(fella.data)) ## ----------------------------------------------------------------------------- date() ## ----------------------------------------------------------------------------- tempfile(pattern = "vignette_mmu_", fileext = ".RData") %T>% message("Saving workspace to ", .) %>% save.image(compress = "xz")