This function combines 'efetchIPG()' and 'IPG2Lineage()' to map a set of protein accessions to their assembly (GCA_ID), tax ID, and lineage.
Function to map protein accession numbers to lineage
This function combines 'efetchIPG()' and 'IPG2Lineage()' to map a set of protein accessions to their assembly (GCA_ID), tax ID, and lineage.
Usage
acc2Lineage(
accessions,
assembly_path,
lineagelookup_path,
ipgout_path = NULL,
plan = "multicore"
)
acc2Lineage(
accessions,
assembly_path,
lineagelookup_path,
ipgout_path = NULL,
plan = "multicore"
)Arguments
- accessions
Character vector of protein accessions
- assembly_path
String of the path to the assembly_summary path This file can be generated using the "downloadAssemblySummary()" function
- lineagelookup_path
String of the path to the lineage lookup file (taxid to lineage mapping). This file can be generated using the
- ipgout_path
Path to write the results of the efetch run of the accessions on the ipg database. If NULL, the file will not be written. Defaults to NULL
- plan
Character. Specifies the execution plan for parallel processing. Default is "multicore".
Value
A data.table that contains the lineage information, mapping protein
accessions to their tax IDs and lineages.
A dataframe containing lineage information mapped to the given protein accessions. The dataframe includes relevant columns such as TaxID, GCA_ID, Protein, Protein Name, Species, and Lineage.
Examples
if (FALSE) { # \dontrun{
acc2Lineage()
} # }
if (FALSE) { # \dontrun{
lineage_data <- acc2Lineage(
accessions = c("P12345", "Q67890"),
assembly_path = "path/to/assembly_summary.txt",
lineagelookup_path = "path/to/lineage_lookup.tsv",
ipgout_path = "path/to/output.txt"
)
} # }