## ----警告= false，消息= false ---------------------------------------------------------------------------------------库（Fella）数据（“ fella.sample”）类（fella.sample）show（fella.sample）## ----警告= false，message，message = false --------------------------------------------------------------数据（“ input.sample”）input.full <-c（input.sample，paste0（“入侵者”，1:10））show（input.full）## ----警告= true，messages = true ---------------------------------------------------------------------------------------------------------- myAnalysis <- defineCompounds( compounds = input.full, data = FELLA.sample)## ----警告= true，消息= true ------------------------------------------------------------------------------------------------ getInput（缅甸分析）## ----警告= true，messages = true ---------------------------------------------------------------------------------------------------- getExcluded(myAnalysis) ## ---- warning=FALSE, message=FALSE, error=TRUE----------------------------------------------------------------------------- paste0（“”，input.full）decorecounds（化合物= input.fail，data = fella.sampe）## ----警告= true，消息= true -------------------------------------------------------------------------------------------------------------------------------------------------------------------缅因分析< - 富集（化合物= input.full，method =“扩散”，大约=“正态”，data = fella.sample）## ----警告= true，messages = true -------------------------------------------------------------------------------------------------- show(new("FELLA.USER")) ## ---- warning=TRUE,消息= true -----------------------------------------------------------------------(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()