parse_ubiome

0th

Percentile

Converts the uBiome file format to taxmap

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: 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_unite_general

Aliases
  • parse_ubiome
Documentation reproduced from package metacoder, version 0.3.3, License: GPL-2 | GPL-3

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