ExtractKEGGPathways_from_UniprotKB.rtf

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\f0\fs24 \cf0 ## Write function to extract KEGG terms\
library(KEGGREST)\
extractKEGGPathways_from_UNIPROTKBs <- function(uniprotkb = uniprotkb, org="mmu")\{\
  \
  # initiate output vector\
  v_KEGGPathways <- character(length(uniprotkb))\
  \
  # go over loop\
  for (i in 1:length(uniprotkb))\{\
      uniprotkb_i  <- uniprotkb[i]\
      uniprot_entry <- paste0("uniprot:",uniprotkb_i) \
     tryCatch(\{\
      keggID <- keggConv(org, uniprot_entry)   # convert uniprotKB to kegg id\
      keggENTRY <- keggGet(keggID)               # extract kegg pathways for kegg id\
      if (is.null(keggENTRY[[1]]$PATHWAY))\{\
        v_KEGGPathways[i] <<- ""\
      \} else \{\
        kegg_entry_collapse <- paste0("KEGG: ", keggENTRY[[1]]$PATHWAY)\
        kegg_entry_collapse <- paste(kegg_entry_collapse, collapse="; ")\
        v_KEGGPathways[i] <- kegg_entry_collapse\
        \
      \}\
    \}, error = function(err) \{\
      v_KEGGPathways[i] <<- ""\
    \})\
  \}\
  \
  # return pathway vector separated by ";"\
  return(v_KEGGPathways)\
\}}