parse_edge_list

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Convert a table with an edge list to taxmap

Converts a table containing an edge list into a [taxa::taxmap()] object. An "edge list" is two columns in a table, where each row defines a taxon-supertaxon relationship. The contents of the edge list will be used as taxon IDs. The whole table will be included as a data set in the output object.

Keywords
internal
Usage
parse_edge_list(input, taxon_id, supertaxon_id, taxon_name,
  taxon_rank = NULL)
Arguments
input

A table containing an edge list encoded by two columns.

taxon_id

The name/index of the column containing the taxon IDs.

supertaxon_id

The name/index of the column containing the taxon IDs for the supertaxon of the IDs in `taxon_col`.

See Also

Other parsers: parse_dada2, parse_greengenes, parse_mothur_tax_summary, parse_mothur_taxonomy, parse_newick, parse_phyloseq, parse_phylo, parse_qiime_biom, parse_rdp, parse_silva_fasta, parse_ubiome, parse_unite_general

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

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