ebimetagenomics (version 0.6)

getRunOtu: Downloads OTU count data associated with a EMG run

Description

This function downloads an OTU count data file associated with a particular run from the EMG portal. The OTU data is returned as a data frame.

Usage

getRunOtu(runID,verb=FALSE,plot.preston=FALSE)

Arguments

runID

A string representing a valid run ID.

verb

If true, outputs runID to console.

plot.preston

If true, produces a Preston plot for the taxa abundance distribution of the run.

Value

An R data frame containing OTU count data. The first column is the OTU ID, the second is the count, and the third contains a taxonomic classification.

See Also

getSampleOtu, mergeOtu, projectRuns, convertOtuTad, plotOtu, read.otu.tsv

Examples

# NOT RUN {
ps=getProjectSummary("SRP047083")
samp=projectSamples(ps)
runs=runsBySample(ps,samp[2])
getRunOtu(runs[1])
# }