subsetTax

subsetTax

R Documentation

Filter results by taxonomy

Description

Create a SQM or SQMbunch object containing only the contigs with a given consensus taxonomy, the ORFs contained in them and the bins that contain them.

Usage

subsetTax(
  SQM,
  rank,
  tax,
  trusted_functions_only = FALSE,
  ignore_unclassified_functions = FALSE,
  rescale_tpm = TRUE,
  rescale_copy_number = TRUE,
  recalculate_bin_stats = FALSE,
  allow_empty = FALSE
)

Arguments

`SQM`	SQM object to be subsetted.
`rank`	character. The taxonomic rank from which to select the desired taxa (`superkingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`)
`tax`	character. A taxon or vector of taxa to be selected.
`trusted_functions_only`	logical. If `TRUE`, only highly trusted functional annotations (best hit + best average) will be considered when generating aggregated function tables. If `FALSE`, best hit annotations will be used (default `FALSE`).
` ignore_unclassified_functions`	logical. If `FALSE`, ORFs with no functional classification will be aggregated together into an “Unclassified” category. If `TRUE`, they will be ignored (default `FALSE`).
`rescale_tpm`	logical. If `TRUE`, TPMs for KEGGs, COGs, and PFAMs will be recalculated (so that the TPMs in the subset actually add up to 1 million). Otherwise, per-function TPMs will be calculated by aggregating the TPMs of the ORFs annotated with that function, and will thus keep the scaling present in the parent object. By default it is set to `TRUE`, which means that the returned TPMs will be scaled by million of reads of the selected taxon.
`rescale_copy_number`	logical. If `TRUE`, copy numbers with be recalculated using the median single-copy gene coverages in the subset. Otherwise, single-copy gene coverages will be taken from the parent object. By default it is set to `TRUE`, which means that the returned copy numbers for each function will represent the average copy number of that function per genome of the selected taxon.
`recalculate_bin_stats`	logical. If `TRUE`, bin abundance, quality and taxonomy are recalculated based on the contigs present in the subsetted object (default `TRUE`).
`allow_empty`	(internal use only).

Value

SQM or SQMbunch object containing only the requested taxon.