as_phyloseq

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Convert taxmap to phyloseq

Convert a taxmap object to a phyloseq object.

Usage
as_phyloseq(obj, otu_table = NULL, otu_id_col = "otu_id",
  sample_data = NULL, sample_id_col = "sample_id", phy_tree = NULL)
Arguments
obj

The taxmap object.

otu_table

The table in `obj$data` with OTU counts. Must be one of the following:

NULL

Look for a table named "otu_table" in `obj$data` with taxon IDs, OTU IDs, and OTU counts. If it exists, use it.

character

The name of the table stored in `obj$data` with taxon IDs, OTU IDs, and OTU counts

data.frame

A table with taxon IDs, OTU IDs, and OTU counts

FALSE

Do not include an OTU table, even if "otu_table" exists in `obj$data`

otu_id_col

The name of the column storing OTU IDs in the otu table.

sample_data

A table containing sample data with sample IDs matching column names in the OTU table. Must be one of the following:

NULL

Look for a table named "sample_data" in `obj$data`. If it exists, use it.

character

The name of the table stored in `obj$data` with sample IDs

data.frame

A table with sample IDs

FALSE

Do not include a sample data table, even if "sample_data" exists in `obj$data`

sample_id_col

The name of the column storing sample IDs in the sample data table.

phy_tree

A phylogenetic tree of class phylo from the ape package with tip labels matching OTU ids. Must be one of the following:

NULL

Look for a tree named "phy_tree" in `obj$data` with tip labels matching OTU ids. If it exists, use it.

character

The name of the tree stored in `obj$data` with tip labels matching OTU ids.

phylo

A tree with tip labels matching OTU ids.

FALSE

Do not include a tree, even if "phy_tree" exists in `obj$data`

Aliases
  • as_phyloseq
Examples
# NOT RUN {
# Install phyloseq to get example data
# source('http://bioconductor.org/biocLite.R')
# biocLite('phyloseq')

# Parse example dataset
library(phyloseq)
data(GlobalPatterns)
x <- parse_phyloseq(GlobalPatterns)

# Convert back to a phylseq object
as_phyloseq(x)

# }
Documentation reproduced from package metacoder, version 0.3.3, License: GPL-2 | GPL-3

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