sub_tax_summary: Subsetting tax summary objects

In LorMe: Lightening One-Code Resolving Microbial Ecology Solution

Subsetting tax summary objects

Description

Subsetting tax summary objects

Usage

sub_tax_summary(taxobj, ..., specificnum = NULL, taxnum = NULL)

Arguments

taxobj	tax summary objects computed by tax_summary.
...	logical expression that are are defined in terms of the variables in Groupfile of tax summary objects. See details in subset.
specificnum	specific numbers indicating samples to keep based on Groupfile of tax summary objects.
taxnum	specific numbers indicating taxonomy to keep based on Base file

Value

Subset of tax summary objects.Same as tax_summary.

Author(s)

Wang Ningqi [e-mail]

Examples

  data("Three_group")

  # Check meta file
  print(Three_group$Groupfile)

  # Subsetting tax summary objects

  # Select BF and OF groups
  sub_testtax_summary <- sub_tax_summary(Three_group, Group %in% c("BF", "OF"))
  print(sub_testtax_summary$Groupfile)

  # Subsetting according to taxonomy

  Proteo <- sub_tax_summary(
    Three_group,
    taxnum = which(Three_group$Base_taxonomy$Phylum == "p__Proteobacteria")
  )
  print(Proteo$Phylum_percent)  # Check phylum table
  print(Proteo$Genus_percent)   # Check genus table

LorMe documentation built on Sept. 13, 2024, 9:07 a.m.