## ----设置，echo = false -------------------------------------------------------------------------------------------------------------------------------------------------- knitr::opts_chunk$set(message=FALSE, fig.path='figures/') ## ----include = FALSE--------------------------------------------------------------------------------------------库（代谢信号）## ----消息= false，整理= true --------------------------------------------------------------------------------------------------------------------------------------------------- MS_keggFinder(KEGG_database="organism", match = "rattus") ## ----tidy = TRUE, tidy.opts=list(indent = 4, width。，有机体=“ rno”）## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- c（“ rno00010”，“ rno00562”）signding_paths <-c（“ rno04910”，“ rno04151”）## -------------------metabo_paths = metabo_paths，＃signming_paths = signming_paths）＃## --------------------------------------------------------------------------------------------------------dent = 4, width.cutoff = 50)--------------- MetaboSignal_table <- MS_replaceNode(node1 = c("cpd:C00267", "cpd:C00221"), node2 = "cpd:C00031", MetaboSignal_table) ## ----tidy = TRUE, tidy.opts=list(indent = 4, width.cutoff = 50), message = FALSE---- MS_findMappedNodes(nodes = c("cpd:C00267", "cpd:C00221", "cpd:C00031"), MetaboSignal_table) ## ----tidy = TRUE, tidy.opts=list(indent = 4, width.cutoff = 50), message = FALSE--- ##获取kegg ids ms_convertgene（genes = c（“ 303565”，“ 65038”，“ 309179”），有机体_code =“ rno”，ankisism_name =“ rat”，输出=“ matrix”）ms_distances（metabosignal_table，enstabosignal_code = sancemissismisism_code = "rno", source_genes = c("K01084", "K15909", "K11584"), target_metabolites = "cpd:C00031", names = TRUE) ## ----tidy = TRUE, tidy.opts=list(indent = 4, width.cutoff = 50), eval = FALSE---- # MS_shortestPathsNetwork(MetaboSignal_table, organism_code="rno", # source_nodes = c("K01084", "K15909", "K11584"), # target_nodes = "cpd:C00031", type = "bw", # file_name = "MS")