toPhyloseq | R Documentation |
Convert abundances to phyloseq object
toPhyloseq( abundances, metadata = NULL, lineages = NULL, assignSampleNames = FALSE, dummyMetadata = FALSE, dummyLineages = FALSE, lineageSource = NULL )
abundances |
a matrix with taxa as rows and samples as columns |
metadata |
an optional data frame with metadata items as columns, where samples are in the same order as in abundances |
lineages |
an optional lineage matrix where row names match row names of taxa; taxa must be provided in the same order as in x; first column gives kingdom, following columns give phylum, class, order, family, genus and species |
assignSampleNames |
assign random sample names |
dummyMetadata |
create a dummy metadata object with a single numeric item from a normal distribution; only if no metadata are provided |
dummyLineages |
assign dummy lineages; only if no lineages are provided and a lineageSource is given |
lineageSource |
a phyloseq object with known lineages, e.g. GlobalPatterns (phyloseq preloaded data that can be loaded with data(GlobalPatterns)), to be used for random lineage assignment |
phyloseq object
data(ibd_taxa) data(ibd_metadata) data(ibd_lineages) phyloseq.obj=toPhyloseq(ibd_taxa,metadata=ibd_metadata,lineages=ibd_lineages) phyloseq.obj
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