convert_hmdb_to_kegg: Convert HMDB codes to KEGG codes.

In specmine: Metabolomics and Spectral Data Analysis and Mining

Description

Converts a vector of HMDB codes into a vector of the corresponding KEGG codes. This is performed by using our internal library used in NMR identification, it will not have all chebi codes.

Usage

convert_hmdb_to_kegg(hmdb_codes)

Arguments

hmdb_codes

Vector with the HMDB codes (each hmdb code must have 7 digits, e.g., HMDB0000001)

Value

Named vector with kegg codes and respective names. Vector names are the compound names and the vector elements the kegg codes.

Examples

keggs=convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246"))
keggs

Example output

Warning messages:
1: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string '(±)-erythro-Isoleucine' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
2: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string '9-cis-β-caroteno' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
3: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string 'Stigmasta-5,22-dien-3ß-ol' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
4: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string 'Ergost-5-en-3ß-ol' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
5: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string '1-naphthyl β-D-glucoside' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
6: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string 'Ergosta-5(22)-dien-3ß-ol' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
7: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string '(6E,9E,12E)-(2-acetoxy -β-D-glucose)-octadecatrienoic acid ester' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
8: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string '(Z)-Stigmasta-5,24(28)-dien-3ß-ol' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
9: In convert_hmdb_to_kegg(c("HMDB0000001", "HMDB0000008", "HMDB0000246")) :
  input string 'Stigmasta-5,28-dien-3ß,24-diol' cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?
    1-Methylhistidine 2-hydroxybutyric acid 
         "cpd:C01152"          "cpd:C05984" 

specmine documentation built on Sept. 21, 2021, 5:06 p.m.