Virusparies (version 1.1.0)

VhgAddPhylum: VhgAddPhylum: extract Phylum information

Description

VhgAddPhylum adds a Phylum column to the provided VirusHunter or VirusGatherer hittable, with each entry in the column reflecting the phylum name derived from the groupby column for each observation.

Usage

VhgAddPhylum(file, groupby = "best_query")

Value

Hittable with Phylum column

Arguments

file

A data frame containing VirusHunter or VirusGatherer hittable results.

groupby

(optional): A character specifying the column containing the groups (default: "best_query"). Note: Gatherer hittables do not have a "best_query" column. Please provide an appropriate column for grouping.

Author

Sergej Ruff

See Also

VirusHunterGatherer is available here: https://github.com/lauberlab/VirusHunterGatherer.

Examples

path <- system.file("extdata", "virushunter.tsv", package = "Virusparies")
vh_file <- ImportVirusTable(path)

vh_file_filtered <- VhgPreprocessTaxa(vh_file,"Family")

processed_taxa <- VhgAddPhylum(vh_file_filtered,"ViralRefSeq_taxonomy")

print(unique(processed_taxa$Phylum))