ebimetagenomics (version 0.6)

getSampleOtu: Downloads and merges all of the OTU count data associated with a EMG sample

Description

This function downloads the OTU count data files from all runs associated with a particular sample from the EMG portal, and merges it using mergeOtu. The merged OTU data is returned as a data frame.

Usage

getSampleOtu(summ,sampleID,verb=TRUE,plot.preston=FALSE)

Arguments

summ

An EMG project summary file, as returned by getProjectSummary.

sampleID

A string representing a valid EMG sample ID within the project summ.

verb

If true, outputs each runID to console.

plot.preston

If true, produces a Preston plot for the taxa abundance distribution of each run as it is downloaded.

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

getRunOtu, mergeOtu, projectSamples, convertOtuTad, plotOtu

Examples

# NOT RUN {
ps=getProjectSummary("SRP108566")
samp=projectSamples(ps)
getSampleOtu(ps,samp[1])
# }