parse_ubiome: Converts the uBiome file format to taxmap

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Converts the uBiome file format to taxmap

Description

Converts the uBiome file format to taxmap. NOTE: This is experimental and might not work if uBiome changes their format. Contact the maintainers if you encounter problems/

Usage

parse_ubiome(file = NULL, table = NULL)

Arguments

file	(character of length 1) The file path to the input file. Either "file", or "table" must be used, but only one.
table	(character of length 1) An already parsed data.frame or tibble. Either "file", or "table" must be used, but only one.

Details

The input file has a format like:

 tax_name,tax_rank,count,count_norm,taxon,parent
 root,root,29393,1011911,1,
 Bacteria,superkingdom,29047,1000000,2,131567
 Campylobacter,genus,23,791,194,72294
 Flavobacterium,genus,264,9088,237,49546

Value

taxmap

See Also

Other parsers: extract_tax_data(), lookup_tax_data(), parse_dada2(), parse_edge_list(), parse_greengenes(), parse_mothur_tax_summary(), parse_mothur_taxonomy(), parse_newick(), parse_phyloseq(), parse_phylo(), parse_qiime_biom(), parse_rdp(), parse_silva_fasta(), parse_tax_data(), parse_unite_general()

metacoder documentation built on April 4, 2023, 9:08 a.m.