Import new RDP OTU-table format
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.
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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.