Example objects for getting started, and related utilities.
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filename for .rda saves of example objects (string)
filename for saved example JSON text (string)
BIOM (Biological Observation Matrix) is a simple prescription for storing an annotated table of data. It may be described as a format, standard, or data structure.
The S3 class
biom and its methods facilitate analyses
by expressing BIOM data as objects in the R environment.
Simple data objects of several kinds are provided to experiment
with handling BIOM in R.
See the examples below.
buildBiomExamples() draws from MG-RAST (see below) to construct
these objects and saves them in designated files.
(This utility is used to build the package.)
exampleBiomFile() returns the path to a file of JSON text
correctly structured as BIOM.
applyBiomMethods() is a utility for testing that simply applies all
biom methods to a given object.
exampleBiomFile() has a useful return value, as described above.
Daniel T. Braithwaite
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str(jtxt) str(smat) str(dmat) str(li1) str(li2) str(li3) exampleBiomFile() xx <- biom (file=exampleBiomFile()) yy <- biom (dmat, quiet=TRUE) zz <- biom (li4) ## Not run: ## this prints a large volume of text: applyBiomMethods(xx) applyBiomMethods (yy) ## this requires package MGRASTer: tt1 <- tempfile() tt2 <- tempfile() buildBiomExamples (tt1, tt2) unlink (tt1) unlink (tt2) ## End(Not run)
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