View source: R/make.phyloseq.R
make.phyloseq | R Documentation |
make.phyloseq
creates a phyloseq
object starting
from data.proc
output. Sample metadata and taxonomic assignments can
be optionally included. If a minimum of two elements are passed to
make.phyloseq
, then a phyloseq objext is returned, otherwise,
data.proc
output will be returned as
otu_table-class
.
A data.frame
can be passed with sample.table
to include sample
metadata. In this case, the row names have to be identical to the sample
names included in the data.proc
output. The safest way to make sure
this is the case is to use:
row.names(sampleTable) <- row.names(dproc$stable)
where
sampleTable
is the data.frame
with the metadata. Note that
this assumes that the samples are in the same order as in the the sequence
table.
make.phyloseq(dproc, sample.table = NULL, tax.table = NULL, phy.tree = NULL)
dproc |
The |
sample.table |
The data.frame with sample metadata |
tax.table |
A matrix with taxonomic assignments (see
|
phy.tree |
A phylogenetic tree (see
|
data.proc
, phyloseq
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