Work with QIIME Output Files in R

Documentation for package ‘qiimer’ version 0.9.4

qiimer-package	qiimer: Read QIIME output files and create plots
biom_raw_data	Extract raw data from a BIOM object.
biom_taxonomy	Extract taxonomy info from a biom object.
dist_get	Retrieve distances from a '"dist"' object.
dist_groups	Create a data frame of distances between groups of items.
dist_subset	Extract parts of a '"dist"' object.
make_otu_table	Create an OTU table.
otu_heatmap	Create a heatmap of OTU counts.
qiimer	qiimer: Read QIIME output files and create plots
rarefaction_stats	Compute summary statistics for collated alpha diversity tables.
read_blast_table	Parse tabular output from BLAST.
read_qiime_distmat	Read a QIIME distance matrix file.
read_qiime_mapping_file	Read a QIIME sample mapping file.
read_qiime_otu_mapping	Parse an OTU mapping file from QIIME.
read_qiime_otu_table	Parse a QIIME OTU table file in "calssic" format.
read_qiime_rarefaction	Read a collated alpha diversity table from QIIME.
relmbeta	Sample dataset from murine gut microbiome
relmbeta_alpha	Shannon diversity measurements from murine gut microbiome
relmbeta_assignments	Taxonomic assignments from murine gut microbiome
relmbeta_biom	BIOM format object from murine gut microbiome
relmbeta_counts	OTU counts from murine gut microbiome
relmbeta_dist	Unweighted UniFrac distances from murine gut microbiome
saturated_rainbow	Saturated rainbow palette.
simplify_assignments	Reformat taxonomic assignments for presentation.
split_assignments	Split taxonomic assignment strings
taxonomic_ranks	Standard taxonomic ranks.