# #设置,回声= FALSE --------------------------------------------------- 库(knitr)选项(宽度= 80)# #——wrap-hook回声= FALSE ----------------------------------------------- hook_output = knit_hooks得到(“输出”)knit_hooks设置美元(输出= (x,选项){#这个钩子函数只有当谱线宽度的选择是使用not NULL如果(!。Null (n <- options$linewidth)) {x = knitr:::split_lines(x) #任何比n宽的行都应该换行if (any(nchar(x) > n)) x = strwrap(x, width = n) x = paste(x, collapse = '\n')}选项 ) }) ## ---- listDatabases ------------------------------------------------------- 图书馆(KEGGREST) listDatabases () ## ---- get_organisms ------------------------------------------------------- org < - keggList(“生物”)头(org) # #——list_queryables ----------------------------------------------------- 可查询< - c (listDatabases(),组织[1],org (2 ]) ## ---- query_hsa,eval = FALSE ----------------------------------------------- ## keggList(“hsa ") ## ---- keggGet ------------------------------------------------------------- 查询< - keggGet (c (hsa: 10458,“ece: Z5100 ")) ## ---- querylength --------------------------------------------------------- 长度(查询)# #——探索 ------------------------------------------------------------- 名称(查询[[1]])查询[[1]][[1]]条目查询美元DBLINKS # #——aaseq --------------------------------------------------------------- keggGet (c(“hsa: 10458”,“ece: Z5100”),“aaseq”)# # # #——ntseq检索氨基酸序列 --------------------------------------------------------------- keggGet (c (hsa: 10458,“ece: Z5100”)、“ntseq”)# # # #检索核苷酸序列,png ----------------------------------------------------------------- png < - keggGet(“hsa05130”、“图像”)t <——tempfile()库(png) writePNG (png, t)如果(互动())browseURL (t) # #——separate_keywords,线宽= 80 ------------------------------------- 头(keggFind(“基因”,c(,“志贺毒素 "))) ## ---- 短语,线宽= 80 --------------------------------------------- 头(keggFind(“基因”,“志贺毒素 ")) ## ---- 公式 ------------------------------------------------------------- 头(keggFind(“复合”,“C7H10O5”,“公式 ")) ## ---- formula2 ------------------------------------------------------------ 头(keggFind(“复合”,“O5C7”,“公式 ")) ## ---- exact_mass ---------------------------------------------------------- keggFind(“复合”,174.05,”exact_mass ") ## ---- mol_weight ---------------------------------------------------------- 头(keggFind(300:310“复合”,“mol_weight ")) ## ---- conv_with_ids ------------------------------------------------------- keggConv(“ncbi-gi”,c(“hsa: 10458”、“ece: Z5100 ")) ## ---- conv_species_kegg_to_geneid ----------------------------------------- 头(keggConv(“生态”、“ncbi-geneid ")) ## ---- conv_species_geneid_to_kegg ----------------------------------------- 头(keggConv(“ncbi-geneid”、“生态 ")) ## ---- keggLink ------------------------------------------------------------ 头(keggLink(“路径”,“保险公司 ")) ## ---- keggLink2 ----------------------------------------------------------- keggLink(“通路”,c(“hsa: 10458”,“ece: Z5100”))