Takes the resulting file of an efetch run on the ipg database and
Takes the resulting file of an efetch run on the ipg database and append lineage, and taxid columns
Usage
IPG2Lineage(
accessions,
ipg_file,
refseq_assembly_path,
genbank_assembly_path,
lineagelookup_path
)
IPG2Lineage(
accessions,
ipg_file,
refseq_assembly_path,
genbank_assembly_path,
lineagelookup_path
)Arguments
- accessions
Character vector of protein accessions
- ipg_file
Path to the file containing results of an efetch run on the ipg database. The protein accession in 'accessions' should be contained in this file
- refseq_assembly_path
String. Path to the RefSeq assembly summary file.
- genbank_assembly_path
String. Path to the GenBank assembly summary file.
- lineagelookup_path
String of the path to the lineage lookup file (taxid to lineage mapping). This file can be generated using the "createLineageLookup()" function
- assembly_path
String of the path to the assembly_summary path This file can be generated using the downloadAssemblySummary function
Value
A data.table with the lineage information for the provided protein
accessions.
A data table containing protein accessions along with their corresponding TaxIDs and lineage information.
Examples
if (FALSE) { # \dontrun{
IPG2Lineage()
} # }
if (FALSE) { # \dontrun{
lins <- IPG2Lineage(
accessions = c("P12345", "Q67890"),
ipg_file = "path/to/ipg_results.txt",
refseq_assembly_path = "path/to/refseq_assembly_summary.txt",
genbank_assembly_path = "path/to/genbank_assembly_summary.txt",
lineagelookup_path = "path/to/lineage_lookup.tsv"
)
} # }