# Tools for Parsing, Manipulating, and Graphing Hierarchical Data

## Documentation for package ‘metacoder’ version 0.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

metacoder-package | Metacoder
arrange_obs | Sort columns of 'taxmap' objects
arrange_taxa | Sort columns of 'taxmap' objects
bryophytes_ex_data | Example dataset of bryophytes
contaminants | Example dataset of comtamination
diverging_palette | The defualt diverging color palette
extract_taxonomy | Extract taxonomy information from sequence headers
extract_taxonomy.default | Extract taxonomy information from sequence headers
extract_taxonomy.DNAbin | Extract taxonomy information from sequence headers
extract_taxonomy.list | Extract taxonomy information from sequence headers
filter_obs | Filter observations with a list of conditions
filter_taxa | Filter taxa with a list of conditions
genbank_ex_data | Fungal ITS Genbank refseq
hierarchies | Get classification of taxa
its1_ex_data | Example of ITS1 fungal data
layout_functions | Layout functions
metacoder | Metacoder
mutate_obs | Add columns to 'taxmap' objects
mutate_taxa | Add columns to 'taxmap' objects
n_obs | Count observations in 'taxmap'
n_obs_1 | Count observation assigned in 'taxmap'
n_subtaxa | Get number of subtaxa
n_subtaxa_1 | Get number of subtaxa
n_supertaxa | Get number of supertaxa
obs | Get observations associated with taxa
obs_data | Return observation data from 'taxmap'
obs_data_colnames | Get column names of obs_data
parse_hmp_qiime | Parse HMP QIIME results
parse_mothur_summary | Parse mothur classification summary file
parse_taxonomy_table | Parse taxonomic data in a tsv/csv file
pr2_ex_data | Example of PR2 SSU data
primersearch | Use EMBOSS primersearch for in silico PCR
primersearch.character | Use EMBOSS primersearch for in silico PCR
primersearch.taxmap | Use EMBOSS primersearch for in silico PCR
print.taxmap | Print a 'taxmap' object
qualitative_palette | The defualt qualitative color palette
quantative_palette | The defualt quantative color palette
rdp_ex_data | Example of RDP Archea data
read_fasta | Read a FASTA file
remove_redundant_names | Remove the redundant taxon names
roots | Get root taxa
sample_frac_obs | Sample a proportion of observations from 'taxmap'
sample_frac_taxa | Sample a proportion of taxa from 'taxmap'
sample_n_obs | Sample n observations from 'taxmap'
sample_n_taxa | Sample n taxa from 'taxmap'
select_obs | Subset columns in a 'taxmap' object
select_taxa | Subset columns in a 'taxmap' object
silva_ex_data | Example dataset from SILVA
subtaxa | Get all subtaxa of a taxon
supertaxa | Get all supertaxa of a taxon
taxmap | Create an instance of 'taxmap'
taxonomic_sample | Recursivly sample a set of taxonomic assignments
taxon_data | Return taxon data from 'taxmap'
taxon_data_colnames | Get column names of taxon_data
transmute_obs | Replace columns in 'taxmap' objects
transmute_taxa | Replace columns in 'taxmap' objects
unite_ex_data_1 | Example of UNITE fungal ITS data
unite_ex_data_2 | Example of UNITE fungal ITS data
unite_ex_data_3 | Example of UNITE fungal ITS data