import_RDP_otu: Import new RDP OTU-table format

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

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))

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.