getSampleOtu: Downloads and merges all of the OTU count data associated...
In ebimetagenomics: EBI Metagenomics Portal
Description
Usage
Arguments
Value
See Also
Examples
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
1
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
1
2
3
ps=getProjectSummary("SRP108566")
samp=projectSamples(ps)
getSampleOtu(ps,samp[1])
ebimetagenomics documentation built on May 2, 2019, 9:29 a.m.
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Description Usage Arguments Value See Also Examples
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
1 | getSampleOtu(summ,sampleID,verb=TRUE,plot.preston=FALSE)
|
Arguments
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. |
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
1 2 3 | ps=getProjectSummary("SRP108566")
samp=projectSamples(ps)
getSampleOtu(ps,samp[1])
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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