iRefR (version 1.13)

convert_protein_ID: Convert Protein Identifier

Description

Convert protein identifiers from one of the following formats: iROG ID, icROG ID, gene ID, RefSeq and UniProt, to any other protein identifier in the list.

On iROGs and icROGs: "iRefIndex" guarantees the non-redundancy of protein information by assigning a different protein identifier (called Redundant Object Group, ROG) to every different protein sequence. This is called the "non-canonical" representation. At the same time, groups of non-redundant proteins might be different isoforms of a given protein, and, in this case, the identifier of one protein of the group (called cROG or canonical ROG) is chosen to represent the entire group of similar proteins. This is called the "canonical" representation of proteins. The iROG and icROG IDs correspond to integer representations of the ROG and cROG, respectively. Most of the "iRefR" functions work with iROGs and icROGs.

Usage

convert_protein_ID(input_id_type, input_id_value, output_id_type, id_conversion_table)

Arguments

input_id_type

Input Type of Protein Identifier: iRefIndex non-canonical ("irogid"), iRefIndex canonical ("icrogid"), UniProt ("uniprotkb"), RefSeq ("refseq"), and GeneID ("entrezgene/locuslink").

input_id_value

Input Protein Identifier (value).

output_id_type

Output Type of Protein Identifier: iRefIndex non-canonical ("irogid"), iRefIndex canonical ("icrogid"), UniProt ("uniprotkb"), RefSeq ("refseq"), and GeneID ("entrezgene/locuslink").

id_conversion_table

Variable storing the ID Conversion Table (generated using "create_id_conversion_table()").

Value

output_id_value

Output Protein Identifier (value).

Examples

     ## Not run: 
#      ## get tables
#      irefindex_80_ecoli = get_irefindex("562", "8.0", tempdir())
#      id_conversion_table_ecoli = create_id_conversion_table(irefindex_80_ecoli,
#  tempdir(), "id_conversion_table_562")
# 
#      ## converting from geneID to uniprotID
#      uniprot_id_value = convert_protein_ID("entrezgene/locuslink", "2986728",
#  "uniprotkb", id_conversion_table_ecoli)
# 
#      ## converting a list of iROG IDs (from version 8.0) to RefSeq IDs
#      irog_list = c("9917588", "9917576", "9917577", "369724", "593426", "3033592")
#      refseq_list = list()
#      for (i in irog_list) {
#      	refseq_list[[i]] = convert_protein_ID("irogid", i, "refseq",
#  id_conversion_table_ecoli)
#      }
#      ## End(Not run)