# #——回声= FALSE ------------------------------------------------------------ knitr: opts_chunk设置(eval =假美元 ) ## ----------------------------------------------------------------------------- # 如果(!“RCy3”% % installed.packages ()) {# install.packages (BiocManager) # BiocManager::安装(“RCy3”)#}#库(RCy3 ) ## ----------------------------------------------------------------------------- # cytoscapePing () ## ----------------------------------------------------------------------------- # openSession() #关闭当前会话(不保存),打开一个会话文件示例 ## ----------------------------------------------------------------------------- # 映射。关口< mapTableColumn(“名字”,“酵母”、“运用”,“Entrez基因 ') ## ----------------------------------------------------------------------------- # 映射。关口[1:3]#前三个条目 ## ----------------------------------------------------------------------------- # # 可以在Cytoscape 3.7.0以上# installApp (STRINGapp ') ## ----------------------------------------------------------------------------- # 字符串。cmd = '字符串查询疾病=“乳腺癌”物种截止= 0.9 =“智人”限制= 150 # commandsGET (string.cmd) # # #更多信息字符串命令:# # commandsHelp(“字符串”)# # commandsHelp(疾病查询的字符串 ') ## ----------------------------------------------------------------------------- # 映射。关口< mapTableColumn(“stringdb::规范名称”,“人类”,“Uniprot-TrEMBL”,运用 ') ## ----------------------------------------------------------------------------- # # 可以在Cytoscape 3.7.0以上# installApp (WikiPathways ') ## ----------------------------------------------------------------------------- # wp。cmd = ' wikipathways import-as-pathway id =“WP254”# commandsGET (wp.cmd) # # # wikipathways命令的更多信息:# # commandsHelp (wikipathways) # # commandsHelp(“wikipathways import-as-pathway ') # ## ----------------------------------------------------------------------------- # 映射。关口< mapTableColumn(‘XrefId’,‘人类’,‘Entrez基因’,‘运用 ') ## ----------------------------------------------------------------------------- # only.mapped.cols < - mapped.cols [complete.cases (mapped.cols),“运用”,放弃= FALSE) # colnames (only.mapped.cols) < - XrefId # loadTableData (only.mapped.cols table.key。列= ' SUID ') ## ----------------------------------------------------------------------------- # ? mapTableColumn ## ----------------------------------------------------------------------------- # # 可以在Cytoscape 3.7.0以上# installApp (BridgeDb ') ## ----------------------------------------------------------------------------- # commandsHelp(“bridgedb”)