addLineage — addLineage • MolEvolvR

addLineage

Usage

addLineage(
  df,
  acc_col = "AccNum",
  assembly_path,
  lineagelookup_path,
  ipgout_path = NULL,
  plan = "multicore"
)

addLineage(
  df,
  acc_col = "AccNum",
  assembly_path,
  lineagelookup_path,
  ipgout_path = NULL,
  plan = "multicore"
)

Arguments

df: Dataframe containing accession numbers. The dataframe should have a column specified by acc_col that contains these accession numbers.
acc_col: Character. The name of the column in df containing accession numbers. Default is "AccNum".
assembly_path: String. The path to the assembly summary file generated using the downloadAssemblySummary() function.
lineagelookup_path: String. The path to the lineage lookup file (taxid to lineage mapping) generated using the create_lineage_lookup() function.
ipgout_path: String. Optional path to save intermediate output files. Default is NULL.
plan: Character. Specifies the execution plan for parallel processing. Default is "multicore".

Value

A data.frame that combines the original df with the lineage information.

A dataframe that combines the original dataframe df with lineage information retrieved based on the provided accession numbers.

Examples

if (FALSE) { # \dontrun{
addLineage()
} # }
if (FALSE) { # \dontrun{
enriched_df <- addLineage(df = my_data,
                           acc_col = "AccNum",
                           assembly_path = "path/to/assembly_summary.txt",
                           lineagelookup_path = "path/to/lineage_lookup.tsv")
} # }