metacoder (version 0.3.7)

parse_edge_list: Convert a table with an edge list to taxmap

Description

Converts a table containing an edge list into a [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.

Converts a table containing an edge list into a [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.

Usage

parse_edge_list(input, taxon_id, supertaxon_id, taxon_name, taxon_rank = NULL)
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`.

taxon_name

xxx

taxon_rank

xxx

See Also

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

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