# # - - - - -设置,回声= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - knitr:: opts_chunk设置美元(消息= FALSE, fig.path =“数据/”)# #——包括= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(MetaboSignal) # #——消息= FALSE,整洁= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MS_FindKEGG (KEGG_database =“有机体”,匹配=鼠属)# #——整洁= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MS_FindKEGG (KEGG_database =“通路”,匹配= c(“醇”、“磷酸肌醇”、“胰岛素信号”,“一种蛋白激酶”),organism_code =“优化”)# #——整洁= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - metabo_paths < - c (“rno00010”、“rno00562”) signaling_paths < - c (“rno04910”、“rno04151”) # #——整洁= TRUE,整洁。选择=列表(缩进= 4、宽度。截止= 70),结果=‘黑名单’,eval = FALSE - - - - - # # # MetaboSignal_table < - MetaboSignal_matrix脂肪tissue-filtered网络(metabo_paths = metabo_paths # signaling_paths = signaling_paths # organism_name =“鼠”,#组织= c(“软组织1”、“软组织2”))# # # Unfiltered-network # MetaboSignal_tableUnfiltered < - MetaboSignal_matrix (metabo_paths = metabo_paths # signaling_paths = signaling_paths) # # #检查signaling-genes被tissue-filtering # neglected_genes < - MS_ChangeNames (setdiff (as.vector (MetaboSignal_tableUnfiltered), # as.vector (MetaboSignal_table)),“汽车”)# # # - - - - -整理= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MetaboSignal_table <——MS_ReplaceNode (node1 = c (“cpd: C00267”、“cpd: C00221”), node2 =“cpd: C00031 MetaboSignal_table) # #——整洁= TRUE,消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MS_FindMappedNodes(节点= c (“cpd: C00267”、“cpd: C00221”、“cpd: C00031”), MetaboSignal_table) # #——整洁= TRUE,消息= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MetaboSignal_distances (MetaboSignal_table organism_code =“优化”,source_genes = c (“303565”、“65038”、“309179”), target_metabolites =“cpd: C00031”,名称= TRUE) # #——整洁= TRUE,整洁。选择=列表(缩进= 4、宽度。截止= 70),eval = FALSE - - - - - #子网< - MetaboSignal_NetworkCytoscape (MetaboSignal_table organism_code =“优化”,# source_genes = c (“303565”、“65038”、“309179”), # target_metabolites =“cpd: C00031”类型=“bw”, # file_name =“MSCytoscape”)