SQM_to_phyloseq

SQM_to_phyloseq

R Documentation

Convert a SQM object into a phyloseq object from the phyloseq package

Description

This function will convert the selected features from a SQM object into a phyloseq object from the phyloseq package. When possible, it will also include the taxonomy of the included features (for functional classifications, the taxonomy table will instead include the description of each feature ID). Optionally, it accepts a meta table that will be passed as provided to the phyloseq object constructor.

Usage

SQM_to_phyloseq(
  SQM,
  features = "genus",
  count = "abund",
  md = NULL,
  nocds = "treat_separately",
  no_partial_classifications = FALSE,
  ignore_unclassified = FALSE,
  ignore_unmapped = FALSE,
  bin_tax_source = "SQM",
  include_seqs = FALSE
)

Arguments

`SQM`	A SQM, SQMbunch or SQMlite object.
`features`	character. Either `"orfs"`, `"contigs"`, `"bins"`, any taxonomic rank included in `SQM$taxa` or any functional classication included in `SQM$functions` (default `"tax"`). Note that a given feature type might not be available in this objects (e.g. `"contigs"` in SQMlite objects originating from a SQM reads project).
`count`	character. Either `"abund"` for raw abundances, `"percent"` for percentages, `"bases"` for raw base counts, `"cov"` for coverages, `"cpm"` for coverages per million reads, `"tpm"` for TPM normalized values or `"copy_number"` for copy numbers (default `"abund"`). Note that a given count type might not available in this object (e.g. TPM or copy number in SQMlite objects originating from a SQM reads project).
`md`	data.frame. A optional data.frame containing metadata for the samples in the SQM object.
`nocds`	character. Either `"treat_separately"` to treat features annotated as No CDS separately, `"treat_as_unclassified"` to treat them as Unclassified or `"ignore"` to ignore them in the output (default `"treat_separately"`).
`no_partial_classifications`	logical. When `features` is a taxonomic rank, treat features not fully classified at the requested level (e.g. “Unclassified bacteroidota” at the class level or below) as fully unclassified. This takes effect before `ignore_unclassified`, so if both are `TRUE` the plot will only contain features that were fully classified at the requested level (default `FALSE`).
`ignore_unclassified`	logical. When `features` is a taxonomic rank or functional category, don’t include unclassified reads in the output (default `FALSE`).
`ignore_unmapped`	logical. Don’t include unmapped reads in the output (default `FALSE`).
`bin_tax_source`	character. Source of taxonomy when `features = "bins"`, either `"SQM"` of `"gtdb"` (default `"gtdb"`).
`include_seqs`	logical. Whether to include sequences or not if creating a microtable from ORFs or contigs (default `FALSE`).

Value

A phyloseq object.