phyloseq: import_qiime_sample_data – R documentation

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import_qiime_sample_data

Import just sample_data file from QIIME pipeline.

Description

QIIME produces several files that can be analyzed in the phyloseq-package, This includes the map-file, which is an important input to QIIME that can also indicate sample covariates. It is converted naturally to the sample_data component data type in phyloseq-package, based on the R data.frame.

Usage

import_qiime_sample_data(mapfilename)

Arguments

mapfilename

(Required). A character string or connection. That is, any suitable file argument to the read.table function. The name of the QIIME map file required for processing pyrosequencing tags in QIIME as well as some of the post-clustering analysis. This is a required input file for running QIIME. Its strict formatting specification is expected by this function, do not attempt to modify it manually once it has worked properly in QIIME.

Details

See import_qiime for more information about QIIME. It is also the suggested function for importing QIIME-produced data files.

Value

A sample_data object.

Examples

mapfile <- system.file("extdata", "master_map.txt", package = "phyloseq")
 import_qiime_sample_data(mapfile)

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23