# #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 (mol_weight“复合”,300:310。 ")) ## ---- conv_with_ids ------------------------------------------------------------ keggConv(“ncbi-proteinid”,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(“途径”、“hsa ")) ## ---- keggLink2 ---------------------------------------------------------------- keggLink(“通路”,c(“hsa: 10458”,“ece: Z5100”))