Tools for Parsing, Manipulating, and Graphing Hierarchical Data


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Documentation for package ‘metacoder’ version 0.1.2

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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