Function to map GCA_ID to TaxID, and TaxID to Lineage

Usage

GCA2Lineage(
  prot_data,
  assembly_path = "/data/research/jravilab/common_data/assembly_summary_genbank.txt",
  lineagelookup_path = "/data/research/jravilab/common_data/lineage_lookup.tsv",
  acc_col = "AccNum"
)

Arguments

prot_data: Dataframe containing a column GCA_ID
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 "createLineageLookup()" function
acc_col: Character. The name of the column in prot_data containing accession numbers. Default is "AccNum".

Value

A dataframe containing the merged information of GCA_IDs, TaxIDs, and their corresponding lineage up to the phylum level. The dataframe will include information from the input prot_data and lineage data.

Note

Currently configured to have at most kingdom and phylum

Author

Samuel Chen, Janani Ravi

Examples

if (FALSE) { # \dontrun{
result <- GCA2Lineage(prot_data = my_prot_data,
                       assembly_path = "path/to/assembly_summary.txt",
                       lineagelookup_path = "path/to/lineage_lookup.tsv")
} # }