MCUFD: Calculate mean codon usage similarity.

In adamd3/codondiffR: Codon usage comparisons across taxa

Calculate mean codon usage similarity.

Description

Compare codon usage between sequences in a codonFreq object with those in a reference database. Mean codon usage frequency difference (MCUFD) is calculated as described in Stedman et al. (2013).

Usage

MCUFD(cFobj, exclude = character(length = 0), minlen = 600, norm = FALSE)

MCUFD_enrich(
  cFres,
  n = NA_real_,
  rank = "Phylum",
  save = FALSE,
  pthresh = NA_real_,
  fname = NA_character_,
  units = "in",
  width = 10,
  height = 7,
  dpi = 600,
  ptype = "heatmap",
  outtab = NULL
)

MCUFD_plot(
  cFres,
  type = "bar",
  n = NA_real_,
  rank = "Phylum",
  fname = NA_character_,
  units = "in",
  width = 10,
  height = 7,
  dpi = 600,
  save = FALSE
)

## S4 method for signature 'codonFreq'
MCUFD(cFobj, exclude = character(length = 0), minlen = 600, norm = FALSE)

Arguments

cFobj	An object of class codonFreq.
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 data be normalised? If TRUE, a normalisation step will be performed. Default = FALSE.

Value

A list of data.frames containing values which indicate the degree of codon usage similarity between the sequences used to construct the codonFreq object and those used to construct the reference database. The reference database entries are in rows and the codonFreq sequences are in columns.

Examples

   virusSet <- readSeq(example = TRUE)
   virusCF <- codonFreq(virusSet)
   exclCod <- c("ATT", "TGT")
   MCUFD_tmp <- MCUFD(virusCF, exclude = exclCod, norm = TRUE)
   range(MCUFD_tmp[[1]]$MCUFD)
   table(MCUFD_tmp[[1]]$Kingdom, useNA = "always")
   MCUFD_tmp[[1]]$Species[1:10]

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