## ----setup, echo=FALSE-------------------------------------------------------- library(knitr) options(width=80) ## ----wrap-hook, echo=FALSE---------------------------------------------------- hook_output = knit_hooks$get('output') knit_hooks$set(output = function(x, options) { # this hook is used only when the linewidth option is not NULL if (!is.null(n <- options$linewidth)) { x = knitr:::split_lines(x) # any lines wider than n should be wrapped if (any(nchar(x) > n)) x = strwrap(x, width = n) x = paste(x, collapse = '\n') } hook_output(x, options) }) ## ----listDatabases------------------------------------------------------------ library(KEGGREST) listDatabases() ## ----get_organisms------------------------------------------------------------ org <- keggList("organism") head(org) ## ----list_queryables---------------------------------------------------------- queryables <- c(listDatabases(), org[,1], org[,2]) ## ----query_hsa, eval=FALSE---------------------------------------------------- # keggList("hsa") ## ----keggGet------------------------------------------------------------------ query <- keggGet(c("hsa:10458", "ece:Z5100")) ## ----querylength-------------------------------------------------------------- length(query) ## ----explore------------------------------------------------------------------ names(query[[1]]) query[[1]]$ENTRY query[[1]]$DBLINKS ## ----aaseq-------------------------------------------------------------------- keggGet(c("hsa:10458", "ece:Z5100"), "aaseq") ## retrieves amino acid sequences ## ----ntseq-------------------------------------------------------------------- keggGet(c("hsa:10458", "ece:Z5100"), "ntseq") ## retrieves nucleotide sequences ## ----png---------------------------------------------------------------------- png <- keggGet("hsa05130", "image") t <- tempfile() library(png) writePNG(png, t) if (interactive()) browseURL(t) ## ----separate_keywords, linewidth=80------------------------------------------ head(keggFind("genes", c("shiga", "toxin"))) ## ----keyphrase, linewidth=80-------------------------------------------------- head(keggFind("genes", "shiga toxin")) ## ----formula------------------------------------------------------------------ head(keggFind("compound", "C7H10O5", "formula")) ## ----formula2----------------------------------------------------------------- head(keggFind("compound", "O5C7", "formula")) ## ----exact_mass--------------------------------------------------------------- keggFind("compound", 174.05, "exact_mass") ## ----mol_weight--------------------------------------------------------------- head(keggFind("compound", 300:310, "mol_weight")) ## ----conv_with_ids------------------------------------------------------------ keggConv("ncbi-proteinid", c("hsa:10458", "ece:Z5100")) ## ----conv_species_kegg_to_geneid---------------------------------------------- head(keggConv("eco", "ncbi-geneid")) ## ----conv_species_geneid_to_kegg---------------------------------------------- head(keggConv("ncbi-geneid", "eco")) ## ----keggLink----------------------------------------------------------------- head(keggLink("pathway", "hsa")) ## ----keggLink2---------------------------------------------------------------- keggLink("pathway", c("hsa:10458", "ece:Z5100"))