getSampleOtu {ebimetagenomics} | R Documentation |
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.
getSampleOtu(summ,sampleID,verb=TRUE,plot.preston=FALSE)
summ |
An EMG project summary file, as returned by |
sampleID |
A string representing a valid EMG sample ID within the project |
verb |
If true, outputs each |
plot.preston |
If true, produces a Preston plot for the taxa abundance distribution of each run as it is downloaded. |
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.
getRunOtu
, mergeOtu
, projectSamples
, convertOtuTad
, plotOtu
ps=getProjectSummary("SRP108566") samp=projectSamples(ps) getSampleOtu(ps,samp[1])