import_RDP_otu {phyloseq} | R Documentation

## Import new RDP OTU-table format

### Description

Recently updated tools on RDP Pyro site make it easier to import Pyrosequencing output into R. The modified tool “Cluster To R Formatter” can take a cluster file (generated from RDP Clustering tools) to create a community data matrix file for distance cutoff range you are interested in. The resulting output file is a tab-delimited file containing the number of sequences for each sample for each OTU. The OTU header naming convention is `"OTU_"` followed by the OTU number in the cluster file. It pads “0”s to make the OTU header easy to sort. The OTU numbers are not necessarily in order.

### Usage

    import_RDP_otu(otufile)

### Arguments

`otufile` | (Optional). A character string indicating the file location of the OTU file, produced/exported according to the instructions above.

### Value

A `otu_table-class` object.

### See Also

An alternative “cluster” file importer for RDP results: `import_RDP_cluster`

The main RDP-pyrosequencing website http://pyro.cme.msu.edu/index.jsp

### Examples

    otufile <- system.file("extdata", "rformat_dist_0.03.txt.gz", package="phyloseq")
    ### the gzipped file is automatically recognized, and read using R-connections
    ex_otu  <- import_RDP_otu(otufile)
    class(ex_otu)
    ntaxa(ex_otu)
    nsamples(ex_otu)
    sample_sums(ex_otu)
    head(t(ex_otu))

[Package phyloseq version 1.30.0 Index]