toPhyloseq: Convert abundances to phyloseq object

In hallucigenia-sparsa/seqgroup: Analysis of Sequencing Data with Groups

Convert abundances to phyloseq object

Description

Convert abundances to phyloseq object

Usage

toPhyloseq(
  abundances,
  metadata = NULL,
  lineages = NULL,
  assignSampleNames = FALSE,
  dummyMetadata = FALSE,
  dummyLineages = FALSE,
  lineageSource = NULL
)

Arguments

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

Value

phyloseq object

Examples

data(ibd_taxa)
data(ibd_metadata)
data(ibd_lineages)
phyloseq.obj=toPhyloseq(ibd_taxa,metadata=ibd_metadata,lineages=ibd_lineages)
phyloseq.obj

hallucigenia-sparsa/seqgroup documentation built on July 6, 2022, 1:11 p.m.