## ---- warning=FALSE, message=FALSE-------------------------------------------- library(FELLA) data("FELLA.sample") class(FELLA.sample) show(FELLA.sample) ## ---- warning=FALSE, message=FALSE-------------------------------------------- data("input.sample") input.full <- c(input.sample, paste0("intruder", 1:10)) show(input.full) ## ---- warning=TRUE, message=TRUE---------------------------------------------- myAnalysis <- defineCompounds( compounds = input.full, data = FELLA.sample) ## ---- warning=TRUE, message=TRUE---------------------------------------------- getInput(myAnalysis) ## ---- warning=TRUE, message=TRUE---------------------------------------------- getExcluded(myAnalysis) ## ---- warning=FALSE, message=FALSE, error=TRUE-------------------------------- input.fail <- paste0(" ", input.full) defineCompounds( compounds = input.fail, data = FELLA.sample) ## ---- warning=TRUE, message=TRUE---------------------------------------------- myAnalysis <- enrich( compounds = input.full, method = "diffusion", approx = "normality", data = FELLA.sample) ## ---- warning=TRUE, message=TRUE---------------------------------------------- show(new("FELLA.USER")) ## ---- warning=TRUE, message=TRUE---------------------------------------------- show(myAnalysis) ## ---- warning=FALSE, message=FALSE-------------------------------------------- myAnalysis <- enrich( compounds = input.full, method = listMethods(), approx = "normality", data = FELLA.sample) show(myAnalysis) ## ---- warning=FALSE, message=TRUE--------------------------------------------- myAnalysis_bis <- runDiffusion( object = myAnalysis, approx = "normality", data = FELLA.sample) show(myAnalysis_bis) ## ---- warning=FALSE, message=TRUE, fig.width=8, fig.height=8------------------ plot( x = myAnalysis, method = "hypergeom", main = "My first enrichment using the hypergeometric test in FELLA", threshold = 1, data = FELLA.sample) ## ---- warning=FALSE, message=TRUE, fig.width=8, fig.height=8------------------ plot( x = myAnalysis, method = "diffusion", main = "My first enrichment using the diffusion analysis in FELLA", threshold = 0.1, data = FELLA.sample) ## ---- warning=FALSE, message=TRUE, fig.width=8, fig.height=8------------------ plot( x = myAnalysis, method = "pagerank", main = "My first enrichment using the PageRank analysis in FELLA", threshold = 0.1, data = FELLA.sample) ## ---- warning=FALSE, message=TRUE, results='asis'----------------------------- myTable <- generateResultsTable( object = myAnalysis, method = "diffusion", threshold = 0.1, data = FELLA.sample) knitr::kable(head(myTable, 20)) ## ---- warning=FALSE, message=TRUE--------------------------------------------- myGraph <- generateResultsGraph( object = myAnalysis, method = "diffusion", threshold = 0.1, data = FELLA.sample) show(myGraph) ## ---- warning=FALSE, message=TRUE, results='asis'----------------------------- myTempDir <- tempdir() myExp_csv <- paste0(myTempDir, "/table.csv") exportResults( format = "csv", file = myExp_csv, method = "pagerank", threshold = 0.1, object = myAnalysis, data = FELLA.sample) test <- read.csv(file = myExp_csv) knitr::kable(head(test)) ## ---- warning=FALSE, message=TRUE, results='asis'----------------------------- myExp_graph <- paste0(myTempDir, "/graph.RData") exportResults( format = "igraph", file = myExp_graph, method = "pagerank", threshold = 0.1, object = myAnalysis, data = FELLA.sample) stopifnot("graph.RData" %in% list.files(myTempDir)) ## ---- warning=FALSE, message=TRUE, results='asis'----------------------------- myExp_pajek <- paste0(myTempDir, "/graph.pajek") exportResults( format = "pajek", file = myExp_pajek, method = "diffusion", threshold = 0.1, object = myAnalysis, data = FELLA.sample) stopifnot("graph.pajek" %in% list.files(myTempDir)) ## ----------------------------------------------------------------------------- sessionInfo()