import_qiime_sample_data {phyloseq} | R Documentation

## 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.

### See Also

`import`

`merge_phyloseq`

`phyloseq`

`import_qiime`

`import_qiime_otu_tax`

`import_env_file`

### Examples

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

[Package phyloseq version 1.28.0 Index]