## ----setup, echo=FALSE-------------------------------------------------------- knitr::opts_chunk$set(message=FALSE, fig.path='figures/') ## ----include = FALSE---------------------------------------------------------- library(MetaboSignal) ## ----message = FALSE, tidy = TRUE--------------------------------------------- MS_keggFinder(KEGG_database="organism", match = "rattus") ## ----tidy = TRUE, tidy.opts=list(indent = 4, width.cutoff = 50)--------------- MS_keggFinder(KEGG_database ="pathway", match = c("glycol", "inositol phosphate","insulin signal", "akt"), organism_code = "rno") ## ----tidy = TRUE-------------------------------------------------------------- metabo_paths <- c("rno00010","rno00562") signaling_paths <- c("rno04910", "rno04151") ## ----tidy = TRUE, tidy.opts=list(indent = 4, width.cutoff = 50), results='asis',eval=FALSE---- # MetaboSignal_table <- MS_keggNetwork(metabo_paths = metabo_paths, # signaling_paths = signaling_paths) # ## ----tidy = TRUE, tidy.opts=list(indent = 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---- ## Get KEGG IDs MS_convertGene(genes = c("303565", "65038", "309179"), organism_code = "rno", organism_name = "rat", output = "matrix") MS_distances(MetaboSignal_table, organism_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")