make.phyloseq: Create a phyloseq object

In carlopacioni/amplicR: An R package to process amplicon data

Create a phyloseq object

Description

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.

Usage

make.phyloseq(dproc, sample.table = NULL, tax.table = NULL, phy.tree = NULL)

Arguments

dproc	The data.proc output
sample.table	The data.frame with sample metadata
tax.table	A matrix with taxonomic assignments (see phyloseq for details)
phy.tree	A phylogenetic tree (see phyloseq for details)

See Also

data.proc, phyloseq

carlopacioni/amplicR documentation built on Aug. 19, 2023, 7:59 p.m.