create_phyloseq: Get Phyloseq Object

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

Create a phyloseq object using a biom file, phylogenetic tree file, and a metadata file. Alternatively, an .Rdata file can be used. For now this function takes output from Qiime. The data provided by this package was processed by the NIH's Nephele pipeline.

Usage

create_phyloseq(biom_file = NULL, tree_file = NULL,
  metadata_file = NULL, treatment_group = NULL, parse_func = NULL,
  rdata_file = NULL, save_rooted_tree = FALSE,
  recursive_save = FALSE)

Arguments

biom_file	A file in the BIOM format. Default: NULL
tree_file	A phylogenetic tree file. This function will generate a rooted tree file if your phylogenetic tree isn't already rooted. Default: NULL
metadata_file	Sample metadata in tab delimited format. It's very important that you make sure that you have a sample_id and TreatmentGroup column in your metadata file. You might otherwise run into problems. Default: NULL
treatment_group	The column number or name in the metadata file that contains the treatment group names. Default: NULL
parse_func	The parse function used to parse taxonomy strings from Greengenes or SILVA database. Default: NULL
rdata_file	A .Rdata file. Default: NULL
save_rooted_tree	A logical that determines weather or not the rooted tree is saved. Default: FALSE
recursive_save	If the directory doesn't exists create the parent directories that don't exist as well. Default: FALSE

Details

This function heavily relies on the phyloseq package to import data into R. It also requires you to use an absolute or relative path to your data files or for your data files to be in the working directory.

It's very important that you make sure that you have a sample_id and TreatmentGroup column in your metadata file.

Value

A phyloseq object, and a phylogenetic tree file if one does not already exist.

See Also

import_biom, phyloseq::sample_data(), phyloseq::phy_tree(), import_qiime_sample_data, merge_phyloseq

root, is.rooted, read.tree, write.tree

root_by_longest_edge

Other Data Importers: create_taxmap

Examples

## Not run: 
if(interactive()){
library(MicrobiomeR)
# Get the datafiles from the package
biom_file <- system.file("extdata", "silva_OTU.biom", package = "MicrobiomeR")
tree_file <- system.file("extdata", "silva.tre", package = "MicrobiomeR")
md_file <- system.file("extdata", "nephele_metadata2.txt", package = "MicrobiomeR")
parse_func <- parse_parse_taxonomy_silva_128
}
# Create a phyloseq object from the data files.
phy_obj <- create_phyloseq(biom_file = biom_file,
                           tree_file = tree_file,
                           metadata_file = md_file,
                           parse_func = parse_func)

## End(Not run)

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.