# # - - - - -设置,回声= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - knitr:: opts_chunk设置美元(消息= FALSE, fig.path =“数据/”)# #——消息= FALSE,整洁= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #加载MetaboSignal库(MetaboSignal) # #——整洁= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #监管交互数据(“regulatory_interactions”)头(regulatory_interactions [c (1、3、5)]) # # KEGG代谢途径的数据(“kegg_pathways”)头(kegg_pathways [2]) # # KEGG信号通路的尾巴(kegg_pathways[2]) # #——整洁= TRUE, eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # # # IDs的人类代谢和信号通路# hsa_paths <——MS_getPathIds (organism_code =“保险公司”)# #——整洁= TRUE,整洁。选择=列表(缩进= 4、宽度。截止= 50)- - - - - - - - - - - - - - - # #创建metabo_paths和signaling_paths向量metabo_paths < - kegg_pathways [kegg_pathways [,“Path_type”= =“新陈代谢”,“Path_id”] signaling_paths <——kegg_pathways [kegg_pathways [,“Path_type”= =“信号”,“Path_id”) # #——整洁= TRUE,整洁。选择=列表(缩进= 4、宽度。截止= 50),结果=‘黑名单’,eval = FALSE - - - - - # # #建立KEGG网络(可能需要一段时间)# keggNet_example <——MS_keggNetwork (metabo_paths、signaling_paths expand_genes = TRUE, # convert_entrez = TRUE) # #——整洁= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #看到网络格式头(keggNet_example) # #——整洁= TRUE,整洁。选择=列表(缩进= 4、宽度。截止= 55)- - - - - - - - - - - - - - - - # #得到所有类型的交互all_types < -独特(unlist (strsplit (keggNet_example,“interaction_type”,“/”))) all_types < - gsub (“k_”、“all_types) # #选择想要互动wanted_types < - setdiff (all_types c(“未知”、“indirect-compound”、“间接影响”、“分离”,“状态改变”,“绑定”,“协会”))打印(wanted_types) #互动,将只保留# #过滤器keggNet_example保留希望交互wanted_types < -粘贴(wanted_types崩溃=“|”)keggNet_clean < - keggNet_example [grep (wanted_types, keggNet_example[3]),) # #——整洁= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #建立监管网络TRRUST交互trrustNet_example < - MS2_ppiNetwork(数据集=“TRRUST”) # #建立监管网络OmniPath交互omnipathNet_example < - MS2_ppiNetwork(数据集=“OmniPath”) # #建立监管网络通过合并OmniPath和TRRUST交互ppiNet_example <——MS2_ppiNetwork(数据集=“所有”)# #看到网络格式头(ppiNet_example) # #——整洁= TRUE,整洁。选择=列表(缩进= 4、宽度。截止= 60),结果=‘黑名单’,eval = FALSE - - - - - # # # #合并网络mergedNet_example <——MS2_mergeNetworks (keggNet_clean ppiNet_example) # #——消息= FALSE,整洁= TRUE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #看到网络格式头(mergedNet_example)