PCA: PCA of codon usage by taxon

In adamd3/codondiffR: Codon usage comparisons across taxa

PCA of codon usage by taxon

Description

Perform PCA on codon usage in a reference database and sequences of unknown taxonomic affinity.

Usage

PCA(
  exclude = character(length = 0),
  minlen = 600,
  norm = FALSE,
  rank = "Phylum",
  corCut = 0.9,
  includeTax = NULL
)

## S4 method for signature 'ANY'
PCA(
  exclude = character(length = 0),
  minlen = 600,
  norm = FALSE,
  rank = "Phylum",
  corCut = 0.9,
  includeTax = NULL
)

Arguments

exclude	A character vector of codons to be excluded from comparisons.
minlen	Numeric, the minimum length of sequence (in codons) to be included in the analysis. Default = 500.
norm	Logical, should the codon abundances be normalised? If TRUE, codon abundances will be converted to codon bias scores, such that the sum of scores for each amino acid sum to 1. Default = FALSE.
rank	Character, taxonomic rank to be used for categorisation. Options are "Domain", "Kingdom", and "Phylum". Default = "Phylum".
corCut	Numeric, correlation cutoff used for dropping codons that exhibit collinearity. Default = 0.9.
includeTax	Character, optional vector of taxa (at the specified rank) to be included in the PCA. If not supplied, all taxa will be used.

Value

An object of class prcomp.

Examples

    exclCod <- c("ATT", "TGT")
    PCA_tmp <- PCA(exclude = exclCod, rank = "Phylum", minlen = 600)
    class(PCA_tmp)

adamd3/codondiffR documentation built on Sept. 3, 2022, 2:26 a.m.