import_RDP_otu: Import new RDP OTU-table format
In phyloseq: Handling and analysis of high-throughput microbiome census data

Description Usage Arguments Value See Also Examples

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.

1	import_RDP_otu(otufile)

otufile

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

A otu_table-class object.

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

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

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))