subsetFun: Filter results by function
In SQMtools: Analyze Results Generated by the 'SqueezeMeta' Pipeline

subsetFun

R Documentation

Filter results by function

Description

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

Usage

subsetFun(
  SQM,
  fun,
  columns = NULL,
  ignore_case = TRUE,
  fixed = FALSE,
  trusted_functions_only = FALSE,
  ignore_unclassified_functions = FALSE,
  rescale_tpm = FALSE,
  rescale_copy_number = FALSE,
  recalculate_bin_stats = FALSE,
  allow_empty = FALSE
)

Arguments

`SQM`	SQM or SQMbunch object to be subsetted.
`fun`	character. Pattern to search for in the different functional classifications.
`columns`	character. Restrict the search to the provided column names from `SQM$orfs$table`. If not provided the search will be performed in all the columns containing functional information (default `NULL`).
`ignore_case`	logical Make pattern matching case-insensitive (default `TRUE`).
`fixed`	logical. If `TRUE`, pattern is a string to be matched as is. If `FALSE` the pattern is treated as a regular expression (default `FALSE`).
`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 (default `FALSE`).
`rescale_copy_number`	logical. If `TRUE`, copy numbers with be recalculated using the RecA/RadA coverages in the subset. Otherwise, RecA/RadA coverages will be taken from the parent object. By default it is set to `FALSE`, which means that the returned copy numbers for each function will represent the average copy number of that function per genome in the parent object.
`recalculate_bin_stats`	logical. If `TRUE`, bin stats and taxonomy are recalculated based on the contigs present in the subsetted object (default `FALSE`).
`allow_empty`	(internal use only).

Value

SQM or SQMbunch object containing only the requested function.

Examples

data(Hadza)
Hadza.iron = subsetFun(Hadza, "iron")
Hadza.carb = subsetFun(Hadza, "Carbohydrate metabolism")
# Search for multiple patterns using regular expressions
Hadza.twoKOs = subsetFun(Hadza, "K00812|K00813", fixed=FALSE)

SQMtools documentation built on April 3, 2025, 6:16 p.m.